[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/19775152/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/19781253/transformed.cor.cli.txt"

nPatients in clinical file=628, in cluster file=615, common to both=612
[1]  73 612
[1] "AMP PEAK  1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          145                           467 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          145                           467 
[1] "AMP PEAK  2(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          140                           472 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          140                           472 
[1] "AMP PEAK  3(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        117                         495 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        117                         495 
[1] "AMP PEAK  4(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           65                           547 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           65                           547 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          154                           458 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          154                           458 
[1] "AMP PEAK  6(7P21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          361                           251 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          361                           251 
[1] "AMP PEAK  7(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           210                            402 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           210                            402 
[1] "AMP PEAK  8(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           254                            358 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           254                            358 
[1] "AMP PEAK  9(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          329                           283 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          329                           283 
[1] "AMP PEAK 10(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           366                            246 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           366                            246 
[1] "AMP PEAK 11(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            40                            572 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            40                            572 
[1] "AMP PEAK 12(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           136                            476 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           136                            476 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            150                             462 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            150                             462 
[1] "AMP PEAK 14(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            399                             213 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            399                             213 
[1] "AMP PEAK 15(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           394                            218 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           394                            218 
[1] "AMP PEAK 16(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           396                            216 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           396                            216 
[1] "AMP PEAK 17(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            570 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            570 
[1] "AMP PEAK 18(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           172                            440 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           172                            440 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         160                          452 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         160                          452 
[1] "AMP PEAK 20(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           144                            468 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           144                            468 
[1] "AMP PEAK 21(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           111                            501 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           111                            501 
[1] "AMP PEAK 22(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         139                          473 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         139                          473 
[1] "AMP PEAK 23(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           278                            334 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           278                            334 
[1] "AMP PEAK 24(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            362                             250 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            362                             250 
[1] "AMP PEAK 25(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            466                             146 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            466                             146 
[1] "AMP PEAK 26(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         468                          144 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         468                          144 
[1] "AMP PEAK 27(20Q13.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            470                             142 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            470                             142 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           242                            370 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           242                            370 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        175                         437 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        175                         437 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          174                           438 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          174                           438 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         591 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         591 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           577 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           577 
[1] "DEL PEAK  6(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           92                           520 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           92                           520 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          118                           494 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          118                           494 
[1] "DEL PEAK  8(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            63                            549 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            63                            549 
[1] "DEL PEAK  9(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          199                           413 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          199                           413 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          221                           391 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          221                           391 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          230                           382 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          230                           382 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          158                           454 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          158                           454 
[1] "DEL PEAK 13(5Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          186                           426 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          186                           426 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          188                           424 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          188                           424 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           79                           533 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           79                           533 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         521 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         521 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           17                           595 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           17                           595 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          288                           324 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          288                           324 
[1] "DEL PEAK 19(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        301                         311 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        301                         311 
[1] "DEL PEAK 20(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           565 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           565 
[1] "DEL PEAK 21(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           83                           529 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           83                           529 
[1] "DEL PEAK 22(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            500 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            500 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           137                            475 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           137                            475 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            159                             453 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            159                             453 
[1] "DEL PEAK 25(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           155                            457 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           155                            457 
[1] "DEL PEAK 26(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           110                            502 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           110                            502 
[1] "DEL PEAK 27(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            91                            521 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            91                            521 
[1] "DEL PEAK 28(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             89                             523 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             89                             523 
[1] "DEL PEAK 29(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           209                            403 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           209                            403 
[1] "DEL PEAK 30(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           215                            397 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           215                            397 
[1] "DEL PEAK 31(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           252                            360 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           252                            360 
[1] "DEL PEAK 32(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           250                            362 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           250                            362 
[1] "DEL PEAK 33(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           247                            365 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           247                            365 
[1] "DEL PEAK 34(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            237                             375 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            237                             375 
[1] "DEL PEAK 35(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            68                            544 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            68                            544 
[1] "DEL PEAK 36(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            83                            529 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            83                            529 
[1] "DEL PEAK 37(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         367                          245 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         367                          245 
[1] "DEL PEAK 38(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            95                            517 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            95                            517 
[1] "DEL PEAK 39(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            368                             244 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            368                             244 
[1] "DEL PEAK 40(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           413                            199 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           413                            199 
[1] "DEL PEAK 41(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           430                            182 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           430                            182 
[1] "DEL PEAK 42(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           425                            187 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           425                            187 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            96                            516 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            96                            516 
[1] "DEL PEAK 44(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           133                            479 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           133                            479 
[1] "DEL PEAK 45(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           212                            400 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           212                            400 
[1] "DEL PEAK 46(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            227                             385 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            227                             385 
[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] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 612 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=105,	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=358,	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=27,	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:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=4,	numeric=FALSE,	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 612 columns, 1 survival variables, and 13 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" "RACE"                 
[13] "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 
 20 106 417  67 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 106 417  67 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 106 417  67 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 106 417  67 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
345 150 115 
[1] "table(vv)"
vv
 N0  N1  N2 
345 150 115 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
345 150 115 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
345 150 115 
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
RACE, nv=4, binary=FALSE, numeric=FALSE
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   107  34
  AMP PEAK  1(1Q31.1) WILD-TYPE 365  87
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          141                           452 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                           34                            87 
$`AMP PEAK  1(1Q31.1) MUTATED`
TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 
       12.66        39.45        43.76        43.76        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-6649 
       45.60        16.57        36.53        32.45        29.19        24.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3561 
       24.69        23.87        56.25         5.03        38.99        13.94 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       78.08        54.02         2.01        47.05        47.01        15.02 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 
       19.00         5.03        10.06        33.07        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3973 
       17.03        27.02        12.99        33.01        21.99        13.05 
TCGA-AA-3994 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E 
       27.02        10.98        32.02        35.01        26.01         2.96 
TCGA-AA-A02Y TCGA-AD-6888 TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4614 
       39.98        15.52        22.42        14.50        17.85         5.65 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       22.36        65.00        12.10        11.74        12.69         3.06 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5349 
       12.20        49.08        37.02        25.02        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-5539 
       15.02         5.03        15.02         2.96        14.99        19.59 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
        1.32        15.12        17.85        12.49         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F 
       12.43        14.30       119.70        92.75        81.37        35.97 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6855 
       98.24        95.18         8.61        31.96        11.11        47.41 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA 
       82.39        74.56        65.85        39.42        18.18         9.93 
TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-4110 
       42.77        21.90        30.28        24.13        13.55        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       15.39        10.39        32.02        46.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3999 
        6.05        19.99        13.94        19.04        19.99        28.04 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 
       23.01        37.02        36.03        31.00        70.03        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.96        38.04        38.56         0.69         0.72 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 
       10.19         9.37         4.73        11.01        13.97        15.02 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 
      129.27        24.13        32.61        20.55         8.61        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 
       13.64        11.97         9.96         0.39         0.69         0.76 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

$`AMP PEAK  1(1Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80         1.61         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       42.90        24.33        42.28        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.02        34.65        14.53        32.91        31.63        30.44 
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-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 
        6.05         6.97        14.01         0.92        50.04        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        37.05        36.00        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        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-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
        0.00        17.03         0.00         0.00        36.03         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03         2.01        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       25.02        24.00        27.02        19.07         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-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G 
       14.99        21.99        34.98         1.02        15.02        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-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       27.42        10.88         0.20        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-4313 TCGA-AZ-4315 
       17.26        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
        1.41        32.94         5.13       106.75        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        1.61         2.14         3.25         3.29         0.07        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         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        20.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 
       13.02        29.06        22.03        32.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       15.02        12.00        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.26        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27         4.80        17.13        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
        3.68         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 TCGA-F4-6569 
       26.47       119.93        60.79       117.07        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        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        8.35        23.51        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       85.48        63.62        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        79.69        10.98        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        17.85        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
        8.42        31.30        11.90        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        19.10        34.49        37.74        10.39        16.83 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
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-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 
       15.95         9.07         1.02        12.00        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97        41.00         1.45        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       21.01        15.02         5.03         8.98        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        57.24        51.48         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
       16.31        16.41        11.51        17.46         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       31.30        28.57        32.19         0.66         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6235 
       12.46        55.76 

  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                         0.39                          0.00 
  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 
                        21.99                         19.99 
[1] "0.4 - 129.3 (22.0)" "0.0 - 148.0 (20.0)"
[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 350 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     96   47
  AMP PEAK  1(1Q31.1) WILD-TYPE  350  115
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON                           96                           350
  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        36         2
  AMP PEAK  1(1Q31.1) WILD-TYPE      86        1       29       137         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1Q31.1) MUTATED           1         6          7         18
  AMP PEAK  1(1Q31.1) WILD-TYPE         2        20         11         65
                               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         37       42        18         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                            29
  STAGE IIA                           36                           137
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           7                            11
  STAGE IIIB                          18                            65
  STAGE IIIC                          17                            37
  STAGE IV                            21                            42
  STAGE IVA                            8                            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  1(1Q31.1) MUTATED     4  21  98  21
  AMP PEAK  1(1Q31.1) WILD-TYPE  16  85 319  46
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  T1                           4                            16
  T2                          21                            85
  T3                          98                           319
  T4                          21                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(1Q31.1) MUTATED    70  39  34
  AMP PEAK  1(1Q31.1) WILD-TYPE 275 111  81
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  N0                          70                           275
  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    97  28
  AMP PEAK  1(1Q31.1) WILD-TYPE 353  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     97   28
  AMP PEAK  1(1Q31.1) WILD-TYPE  353   60
   clus
vv  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  0                          97                           353
  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 226 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     61   84
  AMP PEAK  1(1Q31.1) WILD-TYPE  226  241
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  FEMALE                          61                           226
  MALE                            84                           241
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED   105  11
  AMP PEAK  1(1Q31.1) WILD-TYPE 341  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED    105   11
  AMP PEAK  1(1Q31.1) WILD-TYPE  341   17
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  NO                          105                           341
  YES                          11                            17
[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                            51
                               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                             51
  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 342   4  26  23
D1V11, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  R0                         100                           342
  R1                           1                             4
  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
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q31.1) MUTATED                                  0     3
  AMP PEAK  1(1Q31.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q31.1) MUTATED                          15    78
  AMP PEAK  1(1Q31.1) WILD-TYPE                        49   214
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     78
                                  clus
vv                                 AMP PEAK  1(1Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED     1  90
  AMP PEAK  1(1Q31.1) WILD-TYPE   4 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED      1   90
  AMP PEAK  1(1Q31.1) WILD-TYPE    4  258
                        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                           258
[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   101  32
  AMP PEAK  2(2Q33.1) WILD-TYPE 371  89
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          133                           460 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                           32                            89 
$`AMP PEAK  2(2Q33.1) MUTATED`
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 
       15.62         1.61        39.45        43.76        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 
       14.53        32.91        30.44        32.71        29.16        24.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3532 
       24.69        23.87        24.92         1.02        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 
       29.00        19.99        50.04        15.02        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3867 TCGA-AA-3971 
       10.06        35.05        33.07         0.00        24.03        16.08 
TCGA-AA-3979 TCGA-AA-A00W TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E 
       24.00        14.99        31.00         1.02        26.01         2.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       21.37        15.52         5.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 
       16.44        16.31        18.84         5.13         3.19         0.07 
TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 
       12.20        85.45         9.99         8.02        29.06         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02         2.96        29.03        21.99        14.99 
TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD 
       45.40        55.92         4.80        17.13         1.48        24.43 
TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 
        7.50         7.76        14.04        26.47        35.97         8.61 
TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 
        1.55         8.35        74.56        63.62        39.42        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX 
       79.69        18.18        12.79        17.85        29.46        32.98 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 
       30.28        24.13        39.48        17.23        10.39        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3591 
       15.39        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3896 
        6.05        19.99        19.99         1.02        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N 
       48.03        28.04         1.02        46.03        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-BM-6198 
       70.03        38.04        38.56         0.69        26.43        10.19 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       12.39        78.12         7.17         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6514 
       27.95         4.01       129.27         2.40        20.91        16.31 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       13.64         9.96        49.51         0.76        12.46        18.28 
TCGA-G5-6572 
       47.08 

$`AMP PEAK  2(2Q33.1) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       13.94        16.57        37.05        37.25        37.02        32.45 
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-A6-6138 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-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02         1.02        37.05        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       19.07        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01        11.01         5.98        19.00        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        19.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 
        0.00        17.03        10.06         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       12.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       40.96         0.07        56.55         0.79         0.72        10.88 
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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       75.95        58.39         1.41         5.65        32.94       106.75 
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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       12.69         3.06         2.14         3.25         3.29        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56       148.01        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       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-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-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       56.09        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        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         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        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        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        47.41        35.31       133.18        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       42.77         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        34.49        37.74        14.50 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        11.84        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        7.07        36.03        20.05        24.00         1.02        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 
       37.02        32.98         0.99         0.99        19.04        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       36.95        13.02        35.01        14.01        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04        17.03         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        9.07         1.02        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
        1.94        38.96        61.97        41.00         1.45         0.72 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81         6.05        33.17         6.97         9.37         4.73 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       21.01        11.01        15.02        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
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-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12        55.76        26.43 

  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 
                        19.99                         20.02 
[1] "0.0 - 129.3 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    91  49
  AMP PEAK  2(2Q33.1) WILD-TYPE 355 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     91   49
  AMP PEAK  2(2Q33.1) WILD-TYPE  355  113
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON                           91                           355
  RECTUM                          49                           113
[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         0
  AMP PEAK  2(2Q33.1) WILD-TYPE      83        1       28       144        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2Q33.1) MUTATED           2         6          3         23
  AMP PEAK  2(2Q33.1) WILD-TYPE         1        20         15         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(2Q33.1) MUTATED           21       15         6         1
  AMP PEAK  2(2Q33.1) WILD-TYPE         33       48        20         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                            28
  STAGE IIA                           29                           144
  STAGE IIB                            0                            10
  STAGE IIC                            2                             1
  STAGE III                            6                            20
  STAGE IIIA                           3                            15
  STAGE IIIB                          23                            60
  STAGE IIIC                          21                            33
  STAGE IV                            15                            48
  STAGE IVA                            6                            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
  AMP PEAK  2(2Q33.1) MUTATED     3  22 100  14
  AMP PEAK  2(2Q33.1) WILD-TYPE  17  84 317  53
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  T1                           3                            17
  T2                          22                            84
  T3                         100                           317
  T4                          14                            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  2(2Q33.1) MUTATED    63  35  41
  AMP PEAK  2(2Q33.1) WILD-TYPE 282 115  74
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  N0                          63                           282
  N1                          35                           115
  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    93  23
  AMP PEAK  2(2Q33.1) WILD-TYPE 357  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     93   23
  AMP PEAK  2(2Q33.1) WILD-TYPE  357   65
   clus
vv  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  0                          93                           357
  1                          23                            65
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    66  74
  AMP PEAK  2(2Q33.1) WILD-TYPE 221 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     66   74
  AMP PEAK  2(2Q33.1) WILD-TYPE  221  251
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  FEMALE                          66                           221
  MALE                            74                           251
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    95  10
  AMP PEAK  2(2Q33.1) WILD-TYPE 351  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     95   10
  AMP PEAK  2(2Q33.1) WILD-TYPE  351   18
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  NO                           95                           351
  YES                          10                            18
[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                              10
  AMP PEAK  2(2Q33.1) WILD-TYPE                            50
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                      49
  AMP PEAK  2(2Q33.1) WILD-TYPE                    97
                               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                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     301
  COLON MUCINOUS ADENOCARCINOMA                             50
  RECTAL ADENOCARCINOMA                                     97
  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   2   8   9
  AMP PEAK  2(2Q33.1) WILD-TYPE 346   3  29  20
D2V11, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  R0                          96                           346
  R1                           2                             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
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(2Q33.1) MUTATED                                  1     2
  AMP PEAK  2(2Q33.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2Q33.1) MUTATED                          21    73
  AMP PEAK  2(2Q33.1) WILD-TYPE                        43   219
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                     73
                                  clus
vv                                 AMP PEAK  2(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED     3  88
  AMP PEAK  2(2Q33.1) WILD-TYPE   2 260
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED      3   88
  AMP PEAK  2(2Q33.1) WILD-TYPE    2  260
                        clus
vv                       AMP PEAK  2(2Q33.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          88
                        clus
vv                       AMP PEAK  2(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           260
[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    87  27
  AMP PEAK  3(5P12) WILD-TYPE 385  94
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        114                         479 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                         27                          94 
$`AMP PEAK  3(5P12) MUTATED`
TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 
       15.62         1.61        43.76        43.43        44.91        45.60 
TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3538 
       37.25        32.45        30.44        20.61         5.03        26.01 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 
       12.99        13.02        24.00         2.01        47.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3854 
       37.05        19.00        19.04        37.02        14.93        36.03 
TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 
        0.99        17.03        24.03        21.99        50.99        26.01 
TCGA-AA-A00F TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       34.03        21.99        10.98        51.98         2.96         2.01 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-A8YK 
       41.00        40.96         5.79        16.44         0.92        18.84 
TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 
        5.65        62.79        49.41        29.56         1.61        12.69 
TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       49.08        25.02        32.02        15.02         2.96        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-A285 
       14.30         4.80        11.38        12.59         7.50         6.12 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6855 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC 
       95.18        31.96        47.41        46.75        74.79        12.79 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
        8.42        30.28        24.13        37.74        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3609 
       86.63        65.98        36.03        46.03        34.03        19.99 
TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       37.02        17.95        17.03        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 
       17.03        25.97        36.03        12.00        31.00         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 
       38.96        41.00        38.04         0.69         0.72         5.03 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A1DD TCGA-EF-5831 TCGA-EI-6514 
       15.02        10.98         5.03        57.24         2.40        16.31 
TCGA-EI-6883 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       11.51         9.96        28.57        32.19         0.53         0.76 

$`AMP PEAK  3(5P12) WILD-TYPE`
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-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.02        34.65        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 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-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
       54.02        14.01         0.92        50.04        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       11.01        36.00         5.03        85.05        26.99        19.04 
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-3855 TCGA-AA-3858 TCGA-AA-3860 
        0.00        33.07         0.00        32.05        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         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         1.02        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-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
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         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88         0.20         0.46        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
       32.94         5.13       106.75        22.36        65.00        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        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         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        1.91       124.27        23.05        20.02        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-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       12.00        16.04        21.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        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         1.32        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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.41        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        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-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-F4-6703 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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
       32.98        31.30        21.90        11.90        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        34.49        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        15.39        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        29.98        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4021 
        1.02        48.03        32.02        19.99        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-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.95         9.07         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
       51.98        49.97        61.97        38.56         1.45        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       15.02         8.98        13.97        27.95        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
        4.01         5.29       126.44        41.36       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-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-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-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       49.51        31.30         0.39         0.66         0.69         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                       0.53                        0.00 
  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 
                      19.79                       19.99 
[1] "0.5 - 95.2 (19.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    77  40
  AMP PEAK  3(5P12) WILD-TYPE 369 122
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     77   40
  AMP PEAK  3(5P12) WILD-TYPE  369  122
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  COLON                         77                         369
  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        18        0        6        27         1
  AMP PEAK  3(5P12) WILD-TYPE      86        1       30       146         9
                             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         2        23         13         71
                             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         38       45        20         1
D3V4, multiclass
            clus
vv           AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  STAGE I                           18                          86
  STAGE IA                           0                           1
  STAGE II                           6                          30
  STAGE IIA                         27                         146
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          3                          23
  STAGE IIIA                         5                          13
  STAGE IIIB                        12                          71
  STAGE IIIC                        16                          38
  STAGE IV                          18                          45
  STAGE IVA                          6                          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
  AMP PEAK  3(5P12) MUTATED     2  25  77  13
  AMP PEAK  3(5P12) WILD-TYPE  18  81 340  54
D3V5, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  T1                         2                          18
  T2                        25                          81
  T3                        77                         340
  T4                        13                          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  3(5P12) MUTATED    55  32  29
  AMP PEAK  3(5P12) WILD-TYPE 290 118  86
D3V6, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  N0                        55                         290
  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    78  24
  AMP PEAK  3(5P12) WILD-TYPE 372  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     78   24
  AMP PEAK  3(5P12) WILD-TYPE  372   64
   clus
vv  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  0                        78                         372
  1                        24                          64
[1] 2 2
[1] FALSE
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    52  65
  AMP PEAK  3(5P12) WILD-TYPE 235 260
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     52   65
  AMP PEAK  3(5P12) WILD-TYPE  235  260
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  FEMALE                        52                         235
  MALE                          65                         260
[1] 2 2
[1] FALSE
D3V9, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    82   9
  AMP PEAK  3(5P12) WILD-TYPE 364  19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     82    9
  AMP PEAK  3(5P12) WILD-TYPE  364   19
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  NO                         82                         364
  YES                         9                          19
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                     68
  AMP PEAK  3(5P12) WILD-TYPE                  314
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                               9
  AMP PEAK  3(5P12) WILD-TYPE                            51
                             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                                  68
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 40
  RECTAL MUCINOUS ADENOCARCINOMA                         0
                                clus
vv                               AMP PEAK  3(5P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   314
  COLON MUCINOUS ADENOCARCINOMA                           51
  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    85   1  13   3
  AMP PEAK  3(5P12) WILD-TYPE 357   4  24  26
D3V11, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  R0                        85                         357
  R1                         1                           4
  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
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(5P12) MUTATED                                  0     1
  AMP PEAK  3(5P12) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5P12) MUTATED                          14    53
  AMP PEAK  3(5P12) WILD-TYPE                        50   239
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(5P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               14
  WHITE                                                   53
                                  clus
vv                                 AMP PEAK  3(5P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 50
  WHITE                                                    239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED     1  63
  AMP PEAK  3(5P12) WILD-TYPE   4 285
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED      1   63
  AMP PEAK  3(5P12) WILD-TYPE    4  285
                        clus
vv                       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        63                         285
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5Q22.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(5Q22.3) MUTATED    56   8
  AMP PEAK  4(5Q22.3) WILD-TYPE 416 113
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           64                           529 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                            8                           113 
$`AMP PEAK  4(5Q22.3) MUTATED`
TCGA-3L-AA1B TCGA-5M-AATE TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 
       15.62        39.45        44.91        45.60        37.25        34.65 
TCGA-A6-4107 TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3679 TCGA-AA-3681 
       32.45        25.08        20.61         5.03        15.02         5.98 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3973 TCGA-AA-3975 
       19.04        14.93        24.03        12.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3994 TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 
       26.01        27.02        40.96         5.79        16.44        33.01 
TCGA-AZ-4684 TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 
       65.00        49.41        11.74        32.02         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6932 
        2.96        14.99        11.01        17.75         1.32        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A28M TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6627 
      130.65        12.59        95.18        31.96        44.68        74.79 
TCGA-NH-A6GB TCGA-QL-A97D TCGA-AF-6655 TCGA-AG-3609 TCGA-AG-3885 TCGA-AG-3896 
       15.65        21.90        20.02        19.99        17.95         1.02 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 
        1.02        25.97        15.95        12.00        31.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 
       38.56         0.69         0.72         5.03        20.55        16.31 
TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6811 
       11.51        11.97        49.51        32.19 

$`AMP PEAK  4(5Q22.3) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         1.61         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       13.94        16.57        37.05        37.02        36.53        14.53 
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-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        56.25         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        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-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3977 
       34.03         2.01        21.99        16.08        50.99        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-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-AD-5900 TCGA-AD-6548 
       22.03        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 
       15.52        56.55         0.79         0.72        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       16.31         0.95        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.65        32.94         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.61        12.69         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        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-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        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-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        17.03        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        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         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       24.43        38.20        92.75        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-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-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        65.85        53.62        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30        30.28        11.90        70.03        24.13 
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        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       37.74        10.39        14.50        16.83        15.39        10.39 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        13.94        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-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 
       19.99        28.04        36.03        14.04        17.03         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-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30        28.57         0.39         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                         0.69                          0.00 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                       130.65                        148.01 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                       19.515                        19.990 
[1] "0.7 - 130.7 (19.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.6"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    45  20
  AMP PEAK  4(5Q22.3) WILD-TYPE 401 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     45   20
  AMP PEAK  4(5Q22.3) WILD-TYPE  401  142
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON                           45                           401
  RECTUM                          20                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(5Q22.3) MUTATED         9        0        2        17         1
  AMP PEAK  4(5Q22.3) WILD-TYPE      95        1       34       156         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(5Q22.3) MUTATED           1         1          2          8
  AMP PEAK  4(5Q22.3) WILD-TYPE         2        25         16         75
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(5Q22.3) MUTATED            7        9         5         0
  AMP PEAK  4(5Q22.3) WILD-TYPE         47       54        21         2
D4V4, multiclass
            clus
vv           AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  STAGE I                              9                            95
  STAGE IA                             0                             1
  STAGE II                             2                            34
  STAGE IIA                           17                           156
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            1                            25
  STAGE IIIA                           2                            16
  STAGE IIIB                           8                            75
  STAGE IIIC                           7                            47
  STAGE IV                             9                            54
  STAGE IVA                            5                            21
  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  4(5Q22.3) MUTATED     1  12  45   7
  AMP PEAK  4(5Q22.3) WILD-TYPE  19  94 372  60
D4V5, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  T1                           1                            19
  T2                          12                            94
  T3                          45                           372
  T4                           7                            60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  4(5Q22.3) MUTATED    32  17  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 313 133 100
D4V6, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  N0                          32                           313
  N1                          17                           133
  N2                          15                           100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    42  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 408  73
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     42   15
  AMP PEAK  4(5Q22.3) WILD-TYPE  408   73
   clus
vv  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  0                          42                           408
  1                          15                            73
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    31  34
  AMP PEAK  4(5Q22.3) WILD-TYPE 256 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     31   34
  AMP PEAK  4(5Q22.3) WILD-TYPE  256  291
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  FEMALE                          31                           256
  MALE                            34                           291
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    48   4
  AMP PEAK  4(5Q22.3) WILD-TYPE 398  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     48    4
  AMP PEAK  4(5Q22.3) WILD-TYPE  398   24
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  NO                           48                           398
  YES                           4                            24
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                     42
  AMP PEAK  4(5Q22.3) WILD-TYPE                  340
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                               3
  AMP PEAK  4(5Q22.3) WILD-TYPE                            57
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                      20
  AMP PEAK  4(5Q22.3) WILD-TYPE                   126
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                                0
  AMP PEAK  4(5Q22.3) WILD-TYPE                             13
D4V10, multiclass
                                clus
vv                               AMP PEAK  4(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                    42
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   20
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     340
  COLON MUCINOUS ADENOCARCINOMA                             57
  RECTAL ADENOCARCINOMA                                    126
  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  4(5Q22.3) MUTATED    45   0   7   0
  AMP PEAK  4(5Q22.3) WILD-TYPE 397   5  30  29
D4V11, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  R0                          45                           397
  R1                           0                             5
  R2                           7                            30
  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"
D4V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(5Q22.3) MUTATED                                  0     0
  AMP PEAK  4(5Q22.3) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5Q22.3) MUTATED                           9    34
  AMP PEAK  4(5Q22.3) WILD-TYPE                        55   258
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  4(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED     1  37
  AMP PEAK  4(5Q22.3) WILD-TYPE   4 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED      1   37
  AMP PEAK  4(5Q22.3) WILD-TYPE    4  311
                        clus
vv                       AMP PEAK  4(5Q22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       AMP PEAK  4(5Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           311
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(6P21.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(6P21.1) MUTATED   116  29
  AMP PEAK  5(6P21.1) WILD-TYPE 356  92
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          145                           448 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           29                            92 
$`AMP PEAK  5(6P21.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       43.43        44.91        36.53        32.45        30.44        29.19 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A56B 
       22.52        25.08        25.18        20.61        23.87        56.25 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3561 
       29.00        29.00        12.99        13.02        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       19.99         2.01        15.02        37.05        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 
       35.05        17.03        10.06        24.03        27.02         2.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F 
       20.98        21.99        27.02         7.96        13.94        34.03 
TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 
       27.02        31.00         2.96        40.96        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 
       14.50         0.95        17.26         5.65        22.36        65.00 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       14.30        15.62         9.99         8.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 
       22.98        30.08        32.02         5.03        15.02        13.02 
TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 
       15.02        19.59        56.09        55.92         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         1.48         4.41         9.04         4.80 
TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K 
       11.38        13.32         7.50        14.04       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6854 
       95.18         8.61        31.96        35.74         1.55         0.53 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6625 
       28.21         8.35        82.39        63.62        39.42        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       46.75        10.98        12.79        29.46        21.90        30.28 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       15.39        65.98        36.03        24.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       34.03         6.05        19.99        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-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 
       36.03         9.07        12.00        31.00         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        6.05         9.37        21.01         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 
       27.95         4.01       129.27        24.13        51.48        20.55 
TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 
       15.85        17.69        49.51        28.57         0.39        18.28 
TCGA-G5-6641 
       26.43 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       43.76        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.02        34.65        14.53        32.91        31.63        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-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        19.04        19.04         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       14.93         0.00         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01        24.00         2.01        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       16.44         0.46         0.92        27.09        16.31        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.85        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       75.95        58.39         1.41        32.94         5.13       106.75 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14        82.95         1.91       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-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-6529 
       11.01        10.06        12.03        45.40        12.26        20.19 
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-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         3.68        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 
       26.47        81.37       119.93        35.97        60.79        11.11 
TCGA-F4-6463 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        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 
       33.67        13.25        47.41        35.31       133.18        23.51 
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-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        35.93        61.91        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       18.18        19.33        19.33         9.93        15.65        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H 
       16.80        42.77        32.98         8.42        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 
       70.03        39.48        17.23        13.55        34.49        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
       32.02         8.02         7.07        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
        2.01        50.04        12.03         0.99        15.95        13.94 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        37.02        15.95         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       41.00        38.04        38.56         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.81        33.17         6.97         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        11.01        15.02        13.97        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        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-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76        12.46        55.76        47.08 

  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       129.27                        148.01 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                        20.55                         19.99 
[1] "0.2 - 129.3 (20.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   100  51
  AMP PEAK  5(6P21.1) WILD-TYPE 346 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    100   51
  AMP PEAK  5(6P21.1) WILD-TYPE  346  111
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  COLON                          100                           346
  RECTUM                          51                           111
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(6P21.1) MUTATED        21        0        4        33         1
  AMP PEAK  5(6P21.1) WILD-TYPE      83        1       32       140         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(6P21.1) MUTATED           1         6          6         26
  AMP PEAK  5(6P21.1) WILD-TYPE         2        20         12         57
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(6P21.1) MUTATED           21       19        12         1
  AMP PEAK  5(6P21.1) WILD-TYPE         33       44        14         1
D5V4, multiclass
            clus
vv           AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  STAGE I                             21                            83
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           33                           140
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           6                            12
  STAGE IIIB                          26                            57
  STAGE IIIC                          21                            33
  STAGE IV                            19                            44
  STAGE IVA                           12                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(6P21.1) MUTATED     6  20 113  15
  AMP PEAK  5(6P21.1) WILD-TYPE  14  86 304  52
D5V5, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  T1                           6                            14
  T2                          20                            86
  T3                         113                           304
  T4                          15                            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  5(6P21.1) MUTATED    67  41  45
  AMP PEAK  5(6P21.1) WILD-TYPE 278 109  70
D5V6, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  N0                          67                           278
  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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   102  31
  AMP PEAK  5(6P21.1) WILD-TYPE 348  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    102   31
  AMP PEAK  5(6P21.1) WILD-TYPE  348   57
   clus
vv  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  0                         102                           348
  1                          31                            57
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    65  89
  AMP PEAK  5(6P21.1) WILD-TYPE 222 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     65   89
  AMP PEAK  5(6P21.1) WILD-TYPE  222  236
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                          65                           222
  MALE                            89                           236
[1] 2 2
[1] FALSE
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   103  11
  AMP PEAK  5(6P21.1) WILD-TYPE 343  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    103   11
  AMP PEAK  5(6P21.1) WILD-TYPE  343   17
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  NO                          103                           343
  YES                          11                            17
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                     90
  AMP PEAK  5(6P21.1) WILD-TYPE                  292
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                               9
  AMP PEAK  5(6P21.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                      50
  AMP PEAK  5(6P21.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                1
  AMP PEAK  5(6P21.1) WILD-TYPE                             12
D5V10, multiclass
                                clus
vv                               AMP PEAK  5(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  5(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     292
  COLON MUCINOUS ADENOCARCINOMA                             51
  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  5(6P21.1) MUTATED   107   0  14   5
  AMP PEAK  5(6P21.1) WILD-TYPE 335   5  23  24
D5V11, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  R0                         107                           335
  R1                           0                             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"
D5V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(6P21.1) MUTATED                                  1     1
  AMP PEAK  5(6P21.1) WILD-TYPE                                0    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P21.1) MUTATED                          15    82
  AMP PEAK  5(6P21.1) WILD-TYPE                        49   210
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     82
                                  clus
vv                                 AMP PEAK  5(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED     0  93
  AMP PEAK  5(6P21.1) WILD-TYPE   5 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      0   93
  AMP PEAK  5(6P21.1) WILD-TYPE    5  255
                        clus
vv                       AMP PEAK  5(6P21.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       AMP PEAK  5(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           255
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P21.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P21.3) MUTATED   277  72
  AMP PEAK  6(7P21.3) WILD-TYPE 195  49
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          349                           244 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                           72                            49 
$`AMP PEAK  6(7P21.3) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.76        43.43        44.91        35.11        45.60        13.94 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3534 
        6.97        38.99         9.07        36.03         0.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       19.99        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3852 
        0.99        36.95        37.02        14.93        10.06         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 
       29.98        18.05        31.00        24.00        24.00        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3994 
       21.99        16.08        34.06        26.01        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U 
       13.94        19.00        34.03        38.04        42.02        17.03 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        32.02        33.04        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J 
        2.96         2.01         5.03         0.92        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.20        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       33.01        17.82        17.26        18.84       109.28        75.95 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       12.10        29.56         5.23         3.19         1.61         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        2.14         3.25         3.29        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       85.45         9.99        20.02        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        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         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       16.04        14.99        12.99        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 
       11.08        11.01        10.06        19.59        55.92        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
        4.80        10.26        24.43        38.20        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 
       12.59       140.38         7.50        44.32       131.51         7.76 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
        6.12        14.04        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       31.96        35.74         1.55        33.67         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
      133.18        28.21        82.39        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        13.78        91.79        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5Z1 
       18.18         9.93        15.65        12.79        17.85         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        30.28        70.03        24.13        39.48        17.23 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       20.02        86.63        65.98         7.07        36.03        24.00 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03        34.03        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       15.95        19.99        13.94        19.99        20.98        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 
        0.99         0.99        19.99        17.95        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        1.02        48.03        19.99        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       46.03         6.02        25.97        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 
        1.02        12.00        31.00        70.03        10.98         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         0.69         0.72        26.43 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       10.19         6.05        33.17         9.37         4.73        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        21.01        11.01         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        27.95        10.98         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
      126.44        41.36        57.24       129.27        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.31        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK  6(7P21.3) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
        9.53        46.65        42.90        24.33        42.28        16.57 
TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       37.05        14.53        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       32.71        27.09         8.38        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
       19.66        61.84         3.02        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        1.02        24.03        37.05         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       34.03        29.00         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 
       23.01        20.98        13.94         6.97         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 
       47.05        47.01        26.99        19.04        19.04        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        38.99         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 
        0.00        33.07        36.03        31.07        53.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       12.99        33.01        26.01         2.01        34.03         2.01 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       50.99        13.05        25.02        24.00        19.07         7.96 
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-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
        0.99        14.99        21.99        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-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W 
        1.02        35.01        39.06        39.98        22.03        41.00 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 
       18.05         0.07        56.55         0.72        10.88         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
       27.09        21.44        17.85        19.33        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
        5.65        32.94         5.13         6.77       100.01        11.74 
TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
       12.69         0.07        12.20        12.76        10.06        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        49.08        51.32        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        21.99        13.02        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        12.26        56.09        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       18.25        16.14        15.58         3.68         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 
        1.51        12.00        11.38       119.70       130.65        13.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       98.24        11.11        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 
       41.42        16.24        13.25        35.31         8.35        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 
       53.62        85.48        22.09        26.04        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV 
       79.69        10.98        19.33        19.33        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-AF-2691 TCGA-AF-2692 
       29.46        32.98        31.30        11.90        43.04        13.55 
TCGA-AF-2693 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       19.10        10.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        8.02        20.05         1.02        34.03         2.01        50.04 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
        7.99         0.99        37.02        32.98        19.04         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95        13.02        14.01        32.02        28.04        14.04 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y 
        3.98        20.98        13.94        23.01        37.02        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       51.98        49.97        61.97        41.00         1.45         1.81 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DG 
        6.97        12.39        15.02        19.99         5.95        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 
       32.61        20.55        19.96        17.00        16.41         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       17.46        49.51         0.53         1.12 

  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                            0                             0 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                       148.01                        139.17 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                       19.990                        20.155 
[1] "0.0 - 148.0 (20.0)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   251 108
  AMP PEAK  6(7P21.3) WILD-TYPE 195  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    251  108
  AMP PEAK  6(7P21.3) WILD-TYPE  195   54
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  COLON                          251                           195
  RECTUM                         108                            54
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(7P21.3) MUTATED        57        1       19        78         3
  AMP PEAK  6(7P21.3) WILD-TYPE      47        0       17        95         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(7P21.3) MUTATED           2        16         12         63
  AMP PEAK  6(7P21.3) WILD-TYPE         1        10          6         20
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(7P21.3) MUTATED           37       43        20         1
  AMP PEAK  6(7P21.3) WILD-TYPE         17       20         6         1
D6V4, multiclass
            clus
vv           AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  STAGE I                             57                            47
  STAGE IA                             1                             0
  STAGE II                            19                            17
  STAGE IIA                           78                            95
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           16                            10
  STAGE IIIA                          12                             6
  STAGE IIIB                          63                            20
  STAGE IIIC                          37                            17
  STAGE IV                            43                            20
  STAGE IVA                           20                             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  6(7P21.3) MUTATED    13  60 247  39
  AMP PEAK  6(7P21.3) WILD-TYPE   7  46 170  28
D6V5, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  T1                          13                             7
  T2                          60                            46
  T3                         247                           170
  T4                          39                            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"
                               vv
clus                             N0  N1  N2
  AMP PEAK  6(7P21.3) MUTATED   173 109  77
  AMP PEAK  6(7P21.3) WILD-TYPE 172  41  38
D6V6, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  N0                         173                           172
  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"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   251  62
  AMP PEAK  6(7P21.3) WILD-TYPE 199  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    251   62
  AMP PEAK  6(7P21.3) WILD-TYPE  199   26
   clus
vv  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  0                         251                           199
  1                          62                            26
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   168 193
  AMP PEAK  6(7P21.3) WILD-TYPE 119 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    168  193
  AMP PEAK  6(7P21.3) WILD-TYPE  119  132
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  FEMALE                         168                           119
  MALE                           193                           132
[1] 2 2
[1] FALSE
D6V9, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   258  20
  AMP PEAK  6(7P21.3) WILD-TYPE 188   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    258   20
  AMP PEAK  6(7P21.3) WILD-TYPE  188    8
     clus
vv    AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  NO                          258                           188
  YES                          20                             8
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                    226
  AMP PEAK  6(7P21.3) WILD-TYPE                  156
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                              24
  AMP PEAK  6(7P21.3) WILD-TYPE                            36
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                     102
  AMP PEAK  6(7P21.3) WILD-TYPE                    44
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                                5
  AMP PEAK  6(7P21.3) WILD-TYPE                              8
D6V10, multiclass
                                clus
vv                               AMP PEAK  6(7P21.3) MUTATED
  COLON ADENOCARCINOMA                                   226
  COLON MUCINOUS ADENOCARCINOMA                           24
  RECTAL ADENOCARCINOMA                                  102
  RECTAL MUCINOUS ADENOCARCINOMA                           5
                                clus
vv                               AMP PEAK  6(7P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     156
  COLON MUCINOUS ADENOCARCINOMA                             36
  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  6(7P21.3) MUTATED   259   4  25  14
  AMP PEAK  6(7P21.3) WILD-TYPE 183   1  12  15
D6V11, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  R0                         259                           183
  R1                           4                             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"
D6V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(7P21.3) MUTATED                                  1     6
  AMP PEAK  6(7P21.3) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P21.3) MUTATED                          42   183
  AMP PEAK  6(7P21.3) WILD-TYPE                        22   109
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(7P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 42
  WHITE                                                    183
                                  clus
vv                                 AMP PEAK  6(7P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED     3 216
  AMP PEAK  6(7P21.3) WILD-TYPE   2 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED      3  216
  AMP PEAK  6(7P21.3) WILD-TYPE    2  132
                        clus
vv                       AMP PEAK  6(7P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         216
                        clus
vv                       AMP PEAK  6(7P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(8P11.23) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.23) MUTATED   160  41
  AMP PEAK  7(8P11.23) WILD-TYPE 312  80
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           201                            392 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                            41                             80 
$`AMP PEAK  7(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 
       15.62        12.66        39.45        43.43        24.33        45.60 
TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 
       13.94        34.65        32.45        32.91        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 
       27.09        25.18        24.16        20.28         9.63        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 
        1.02        35.01         6.97         1.02        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 
        0.00        29.00        26.01        12.99        33.99        20.98 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       50.04        47.01         5.98        37.05        19.00         5.03 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 
       19.04        19.04        10.06        36.95        17.03         0.00 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       31.07        31.07        24.03        18.05        12.99        24.00 
TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A01D 
       34.06        24.00        18.05         0.99        21.99        10.98 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 
        1.02        37.02        51.98         0.92         0.07         5.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L 
       27.42        16.44        27.09        16.31        21.44        17.26 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.65        32.94         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       88.21        49.41         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        2.14         3.29         0.07       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         1.91        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 
        1.32         4.80        17.13        16.14         1.48        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-A285 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 
        7.50        44.32         6.12       117.07        98.24        35.74 
TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 
        6.18        16.24        67.30        65.85        53.62        63.62 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       39.42        26.43        46.75        74.79        18.18        15.65 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-3911 
       29.46        32.98         8.42        30.28        70.03        37.74 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 
       20.02        10.39        65.98        36.03        36.03        24.00 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 
       34.03        34.03         2.01         0.99        36.95        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
        1.02        48.03        32.02        36.03         1.02        46.03 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       15.95        31.00        51.98        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        0.72         6.05         9.37         4.73        78.12         7.17 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
       15.02        27.95        10.98         4.01        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 
       24.13        51.48         0.49        17.00        15.85        16.31 
TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       11.51        10.78        49.51        28.57        32.19         0.69 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
       12.46        18.28        47.08 

$`AMP PEAK  7(8P11.23) WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        4.80         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-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       37.25        37.02        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       29.19        33.53        23.61        22.09        22.06        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         5.03         7.04         3.02         1.02 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       58.03        63.98        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       24.03        37.05         8.05        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 
       29.95        23.01        19.99        13.94        61.02         2.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3697 
        0.92        47.05        15.02        11.01        36.00        85.05 
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-3844 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        37.02        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00        33.07        36.03        32.05         0.99        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        27.02        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        50.99        13.05        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02        17.03        14.99        34.98         1.02 
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-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02        35.01        33.04        35.01        26.01        39.06 
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-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72        22.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.92        14.50         0.95        33.01        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       11.74         3.25        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        85.45        70.16         9.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       22.03        30.08        17.03        12.00         2.96        16.04 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        19.59        56.09        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
       18.25        43.27        15.12        17.85        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
        3.68         4.41         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       95.18         8.61        31.96        11.11        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        44.68        55.04        85.48        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       61.91        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        91.79        79.69        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 
        9.93        12.79        17.85        16.80        42.77        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        11.90        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        86.63        11.84        12.00        32.02         8.02 
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-3611 TCGA-AG-3612 
       12.03         6.05        15.95        19.99        13.94        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-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        13.02        14.01        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.97        41.00         1.45        26.43         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       33.17         6.97        12.39        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
        5.03         8.98        13.97        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
        5.29       126.44       129.27        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       19.96        20.91        18.28        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
        8.61        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       31.30         0.39         0.66         0.53         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                             0                              0 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                         20.02                          19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   157  53
  AMP PEAK  7(8P11.23) WILD-TYPE 289 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    157   53
  AMP PEAK  7(8P11.23) WILD-TYPE  289  109
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  COLON                           157                            289
  RECTUM                           53                            109
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(8P11.23) MUTATED        37        0       17        53         4
  AMP PEAK  7(8P11.23) WILD-TYPE      67        1       19       120         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.23) MUTATED           3         8          4         25
  AMP PEAK  7(8P11.23) WILD-TYPE         0        18         14         58
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.23) MUTATED           24       22         9         0
  AMP PEAK  7(8P11.23) WILD-TYPE         30       41        17         2
D7V4, multiclass
            clus
vv           AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  STAGE I                              37                             67
  STAGE IA                              0                              1
  STAGE II                             17                             19
  STAGE IIA                            53                            120
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                             8                             18
  STAGE IIIA                            4                             14
  STAGE IIIB                           25                             58
  STAGE IIIC                           24                             30
  STAGE IV                             22                             41
  STAGE IVA                             9                             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  7(8P11.23) MUTATED     4  38 143  24
  AMP PEAK  7(8P11.23) WILD-TYPE  16  68 274  43
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  T1                            4                             16
  T2                           38                             68
  T3                          143                            274
  T4                           24                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(8P11.23) MUTATED   119  46  43
  AMP PEAK  7(8P11.23) WILD-TYPE 226 104  72
D7V6, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  N0                          119                            226
  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"
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   148  31
  AMP PEAK  7(8P11.23) WILD-TYPE 302  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    148   31
  AMP PEAK  7(8P11.23) WILD-TYPE  302   57
   clus
vv  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  0                          148                            302
  1                           31                             57
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED    95 115
  AMP PEAK  7(8P11.23) WILD-TYPE 192 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED     95  115
  AMP PEAK  7(8P11.23) WILD-TYPE  192  210
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  FEMALE                           95                            192
  MALE                            115                            210
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   153  11
  AMP PEAK  7(8P11.23) WILD-TYPE 293  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    153   11
  AMP PEAK  7(8P11.23) WILD-TYPE  293   17
     clus
vv    AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  NO                           153                            293
  YES                           11                             17
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                    140
  AMP PEAK  7(8P11.23) WILD-TYPE                  242
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                              16
  AMP PEAK  7(8P11.23) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                      51
  AMP PEAK  7(8P11.23) WILD-TYPE                    95
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                                2
  AMP PEAK  7(8P11.23) WILD-TYPE                             11
D7V10, multiclass
                                clus
vv                               AMP PEAK  7(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                    140
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  7(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      242
  COLON MUCINOUS ADENOCARCINOMA                              44
  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  7(8P11.23) MUTATED   144   1  16  15
  AMP PEAK  7(8P11.23) WILD-TYPE 298   4  21  14
D7V11, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  R0                          144                            298
  R1                            1                              4
  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"
D7V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(8P11.23) MUTATED                                  0     5
  AMP PEAK  7(8P11.23) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8P11.23) MUTATED                          20   112
  AMP PEAK  7(8P11.23) WILD-TYPE                        44   180
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     112
                                  clus
vv                                 AMP PEAK  7(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED     1 128
  AMP PEAK  7(8P11.23) WILD-TYPE   4 220
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED      1  128
  AMP PEAK  7(8P11.23) WILD-TYPE    4  220
                        clus
vv                       AMP PEAK  7(8P11.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       AMP PEAK  7(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            220
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(8P11.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(8P11.21) MUTATED   197  47
  AMP PEAK  8(8P11.21) WILD-TYPE 275  74
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           244                            349 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                            47                             74 
$`AMP PEAK  8(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       15.62        12.66        39.45        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 
       24.33        35.11        45.60        13.94        34.65        32.45 
TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6648 
       31.63        23.61        32.71        29.16        27.09        25.18 
TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 
       24.16        20.28        61.84         9.63         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 
        1.02        35.01         6.97         1.02        36.03        19.07 
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-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 
       13.02        24.00        20.98        19.99        19.99        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
        5.98        37.05        19.00        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 
       19.04        10.06        36.95        17.03         0.00        31.07 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        18.05         2.01        12.99        24.00 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       16.08        34.06        24.00        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
       17.03        21.99         1.02        37.02        51.98         0.92 
TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 
       41.00         0.07         5.79        27.42        16.44         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       27.09        21.44        17.26        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36        62.79        88.21        49.41         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 
        3.19         1.61        12.69         3.06         2.14         0.07 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 
       14.30       148.01        15.62        49.08        51.32         1.91 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02        25.02         8.02        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-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       15.02        29.03        14.99        12.99        13.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.08        10.06        55.92        20.19         1.32 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        4.80        17.13        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 
      119.70        38.20       130.65         7.50        44.32         6.12 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
      117.07        98.24         8.61        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       34.42        16.24         8.35        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       44.68        63.62        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 
       30.28        70.03        20.02        10.39        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-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       23.01        15.95         9.07         1.02        31.00        64.01 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98         1.94        38.96        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         9.37         4.73        78.12 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        7.17        13.97        15.02        27.95        10.98         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       126.44        41.36        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        0.49        17.00        15.85        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       13.64        49.51        28.57        32.19         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK  8(8P11.21) WILD-TYPE`
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-A6-3810 
       44.91        16.57        37.05        37.25        37.02        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       14.53        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-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       58.03        63.98        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05         8.05         0.00        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3561 
        0.99        21.01        17.95        29.95        23.01        13.94 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       61.02         6.05         2.01         0.92        47.05        11.01 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       85.05        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 
       31.07        53.00        17.03        29.98        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       21.99        50.99        13.05        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        35.01        26.01        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       33.01        17.82        17.85        19.33        18.84       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 
       75.95        58.39         1.41         5.65        65.00         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
       12.10       100.01        29.56         3.25         3.29        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 
       12.76        10.06        17.56        85.45        70.16         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 
       21.14        82.95       124.27        23.05        26.04        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       29.06        22.03        17.03        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       21.99        15.02        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 
       12.03        45.40        12.26        19.59        56.09        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       17.75        18.25        43.27        15.12        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
        3.68         9.44        11.64         1.51        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-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-A28M TCGA-F4-6460 TCGA-F4-6461 
      119.93        35.97        60.79        95.18        31.96        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        41.42        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       47.41        35.31       133.18        28.21        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       65.85        55.04        85.48        35.93        61.91        36.00 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
       79.69        19.33        19.33         9.93        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 
       16.80        42.77        31.30        21.90        11.90        24.13 
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        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       37.74        10.39        14.50        16.83        15.39        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       11.84        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       46.03        34.03        50.04        12.03         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        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-3885 
       29.98        37.02         0.99         0.99        19.99        17.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-4001 
       17.03        13.02        35.01        14.01        19.99        36.03 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       37.02        36.03        12.00        70.03        10.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00        26.43         1.81        10.19        33.17 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        6.97        12.39        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG TCGA-DY-A1H8 
        8.98        19.99         5.95         5.29        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        2.40        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.34        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        31.30         0.39         0.66         0.69         0.53 
TCGA-F5-6861 
        1.12 

  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                         19.99                          19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   184  70
  AMP PEAK  8(8P11.21) WILD-TYPE 262  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    184   70
  AMP PEAK  8(8P11.21) WILD-TYPE  262   92
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  COLON                           184                            262
  RECTUM                           70                             92
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8P11.21) MUTATED        41        0       21        66         4
  AMP PEAK  8(8P11.21) WILD-TYPE      63        1       15       107         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8P11.21) MUTATED           3        10          7         31
  AMP PEAK  8(8P11.21) WILD-TYPE         0        16         11         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8P11.21) MUTATED           23       34         9         0
  AMP PEAK  8(8P11.21) WILD-TYPE         31       29        17         2
D8V4, multiclass
            clus
vv           AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  STAGE I                              41                             63
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                            66                            107
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            10                             16
  STAGE IIIA                            7                             11
  STAGE IIIB                           31                             52
  STAGE IIIC                           23                             31
  STAGE IV                             34                             29
  STAGE IVA                             9                             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  8(8P11.21) MUTATED     5  45 176  27
  AMP PEAK  8(8P11.21) WILD-TYPE  15  61 241  40
D8V5, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  T1                            5                             15
  T2                           45                             61
  T3                          176                            241
  T4                           27                             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  8(8P11.21) MUTATED   143  56  53
  AMP PEAK  8(8P11.21) WILD-TYPE 202  94  62
D8V6, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  N0                          143                            202
  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"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   178  43
  AMP PEAK  8(8P11.21) WILD-TYPE 272  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    178   43
  AMP PEAK  8(8P11.21) WILD-TYPE  272   45
   clus
vv  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  0                          178                            272
  1                           43                             45
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   111 143
  AMP PEAK  8(8P11.21) WILD-TYPE 176 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    111  143
  AMP PEAK  8(8P11.21) WILD-TYPE  176  182
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  FEMALE                          111                            176
  MALE                            143                            182
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   184  11
  AMP PEAK  8(8P11.21) WILD-TYPE 262  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    184   11
  AMP PEAK  8(8P11.21) WILD-TYPE  262   17
     clus
vv    AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  NO                           184                            262
  YES                           11                             17
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                    164
  AMP PEAK  8(8P11.21) WILD-TYPE                  218
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                              19
  AMP PEAK  8(8P11.21) WILD-TYPE                            41
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                      65
  AMP PEAK  8(8P11.21) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                                3
  AMP PEAK  8(8P11.21) WILD-TYPE                             10
D8V10, multiclass
                                clus
vv                               AMP PEAK  8(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                    164
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  8(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      218
  COLON MUCINOUS ADENOCARCINOMA                              41
  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  8(8P11.21) MUTATED   173   2  22  16
  AMP PEAK  8(8P11.21) WILD-TYPE 269   3  15  13
D8V11, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  R0                          173                            269
  R1                            2                              3
  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"
D8V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(8P11.21) MUTATED                                  0     5
  AMP PEAK  8(8P11.21) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8P11.21) MUTATED                          23   132
  AMP PEAK  8(8P11.21) WILD-TYPE                        41   160
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK  8(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED     1 149
  AMP PEAK  8(8P11.21) WILD-TYPE   4 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED      1  149
  AMP PEAK  8(8P11.21) WILD-TYPE    4  199
                        clus
vv                       AMP PEAK  8(8P11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       AMP PEAK  8(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            199
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8Q12.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(8Q12.1) MUTATED   250  66
  AMP PEAK  9(8Q12.1) WILD-TYPE 222  55
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          316                           277 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                           66                            55 
$`AMP PEAK  9(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2674 
       15.62        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       43.43        24.33        35.11        45.60        13.94        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       29.19        32.71        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A5ZU 
       25.18        24.16        24.69        23.87        20.28         9.63 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02        36.03        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 
       36.00         5.03        19.04        19.04        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        33.07         0.00         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       12.99        24.00        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       26.01        24.00        27.02        13.94        19.00        18.05 
TCGA-AA-A00L TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01K 
       38.04         0.99        17.03        21.99        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        1.02        51.98         2.96         5.03         0.92        41.00 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.07        15.52         5.79        27.42         0.20        16.44 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
        0.92        27.09        16.31        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28        32.94         5.13       106.75        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-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        0.07        14.30       148.01        15.62        49.08        51.32 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
        1.91        20.02        37.02        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       29.03        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.08        11.08        10.06        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19         1.32        43.27        15.12         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         1.48         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04         4.80        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F 
      130.65       140.38         7.50        44.32         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 
       35.74         6.18        34.42        16.24         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       63.62        39.42        35.93        36.00        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW 
       74.79        18.18        10.98         9.93        15.65        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42        30.28        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 
       17.23        43.04        34.49        37.74        10.39        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       10.39        65.98        36.03        32.02        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03        34.03        34.03         6.05         0.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
       19.99         7.99        37.02        32.98        19.04         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95         1.02        48.03        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03         3.98        46.03        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       64.01        51.98         1.94        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        1.45         0.69         0.72        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        4.73        78.12         7.17         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        27.95        10.98         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 
       41.36        57.24        24.13         0.49        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       16.34        16.31        11.51        10.78        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       49.51        28.57         0.39        32.19         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK  9(8Q12.1) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
        4.80        43.76        46.65        42.90        42.28        44.91 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       37.05        34.65        14.53        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       22.09        22.06        22.52         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       24.39        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       56.25         7.04         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 
       23.01        19.99        13.94        61.02         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       47.05        11.01        19.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 
       14.93         0.00        10.06         0.00        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.07        53.00        31.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
        2.01        20.98        21.99        50.99        13.05        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
       19.07         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-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
        1.02        15.02        10.98        32.02        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        39.98         2.01        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       40.96        21.37        56.55         0.79         0.72        22.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       10.88         0.46        14.50         0.95        33.01        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33        75.95        58.39         1.41         5.65 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        6.77       100.01         3.25         3.29        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
       10.06        17.56        85.45        70.16         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 
       82.95       124.27        23.05        26.04        22.03        12.00 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       16.04        15.02        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.03        45.40        19.59        20.42        17.75        18.25 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       17.85        12.49         3.68         9.44        11.64         1.51 
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-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-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 
       81.37       119.93        95.18        11.11        47.87         1.55 
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-G4-6294 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
      133.18        28.21        82.39        85.48        61.91        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        79.69 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33        12.79        17.85        16.80        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       31.30        21.90        11.90        13.55        19.10        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
       16.83        15.39        86.63        11.84        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07        20.05        34.03         2.01        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        13.94        20.98         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        17.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 
       35.01        14.01        19.99        36.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
        6.02        36.03        12.00        10.98        49.97        38.96 
TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
       41.00        26.43         1.81        33.17         6.97        12.39 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       21.01        11.01        15.02        19.99         5.95         5.29 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        51.48        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       20.91        18.28        17.69        16.41         8.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       11.97         8.45        31.30         0.66         0.69         0.53 
TCGA-F5-6861 
        1.12 

  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                       148.01                        139.17 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                        20.02                         19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   236  93
  AMP PEAK  9(8Q12.1) WILD-TYPE 210  69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    236   93
  AMP PEAK  9(8Q12.1) WILD-TYPE  210   69
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON                          236                           210
  RECTUM                          93                            69
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(8Q12.1) MUTATED        48        0       22        87         4
  AMP PEAK  9(8Q12.1) WILD-TYPE      56        1       14        86         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(8Q12.1) MUTATED           3        11         10         45
  AMP PEAK  9(8Q12.1) WILD-TYPE         0        15          8         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q12.1) MUTATED           33       45        14         0
  AMP PEAK  9(8Q12.1) WILD-TYPE         21       18        12         2
D9V4, multiclass
            clus
vv           AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  STAGE I                             48                            56
  STAGE IA                             0                             1
  STAGE II                            22                            14
  STAGE IIA                           87                            86
  STAGE IIB                            4                             6
  STAGE IIC                            3                             0
  STAGE III                           11                            15
  STAGE IIIA                          10                             8
  STAGE IIIB                          45                            38
  STAGE IIIC                          33                            21
  STAGE IV                            45                            18
  STAGE IVA                           14                            12
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(8Q12.1) MUTATED     7  53 231  37
  AMP PEAK  9(8Q12.1) WILD-TYPE  13  53 186  30
D9V5, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  T1                           7                            13
  T2                          53                            53
  T3                         231                           186
  T4                          37                            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  9(8Q12.1) MUTATED   176  79  72
  AMP PEAK  9(8Q12.1) WILD-TYPE 169  71  43
D9V6, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  N0                         176                           169
  N1                          79                            71
  N2                          72                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   227  59
  AMP PEAK  9(8Q12.1) WILD-TYPE 223  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    227   59
  AMP PEAK  9(8Q12.1) WILD-TYPE  223   29
   clus
vv  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  0                         227                           223
  1                          59                            29
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   149 180
  AMP PEAK  9(8Q12.1) WILD-TYPE 138 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    149  180
  AMP PEAK  9(8Q12.1) WILD-TYPE  138  145
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  FEMALE                         149                           138
  MALE                           180                           145
[1] 2 2
[1] FALSE
D9V9, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   233  18
  AMP PEAK  9(8Q12.1) WILD-TYPE 213  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    233   18
  AMP PEAK  9(8Q12.1) WILD-TYPE  213   10
     clus
vv    AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  NO                          233                           213
  YES                          18                            10
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                    212
  AMP PEAK  9(8Q12.1) WILD-TYPE                  170
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                              23
  AMP PEAK  9(8Q12.1) WILD-TYPE                            37
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                      87
  AMP PEAK  9(8Q12.1) WILD-TYPE                    59
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                                4
  AMP PEAK  9(8Q12.1) WILD-TYPE                              9
D9V10, multiclass
                                clus
vv                               AMP PEAK  9(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   212
  COLON MUCINOUS ADENOCARCINOMA                           23
  RECTAL ADENOCARCINOMA                                   87
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     170
  COLON MUCINOUS ADENOCARCINOMA                             37
  RECTAL ADENOCARCINOMA                                     59
  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  9(8Q12.1) MUTATED   227   3  27  17
  AMP PEAK  9(8Q12.1) WILD-TYPE 215   2  10  12
D9V11, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  R0                         227                           215
  R1                           3                             2
  R2                          27                            10
  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"
D9V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q12.1) MUTATED                                  0     5
  AMP PEAK  9(8Q12.1) WILD-TYPE                                1     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q12.1) MUTATED                          35   169
  AMP PEAK  9(8Q12.1) WILD-TYPE                        29   123
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK  9(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED     3 196
  AMP PEAK  9(8Q12.1) WILD-TYPE   2 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED      3  196
  AMP PEAK  9(8Q12.1) WILD-TYPE    2  152
                        clus
vv                       AMP PEAK  9(8Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         196
                        clus
vv                       AMP PEAK  9(8Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           152
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(8Q24.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8Q24.21) MUTATED   276  77
  AMP PEAK 10(8Q24.21) WILD-TYPE 196  44
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           353                            240 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                            77                             44 
$`AMP PEAK 10(8Q24.21) MUTATED`
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-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.76        43.43        24.33        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       16.57        37.25        37.02        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       32.91        31.63        29.19        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       24.69        23.87        20.28        56.25         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05         1.02        35.01         6.97         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       24.03        36.03        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        20.98        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 
        5.98        37.05        36.00         5.03        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 
       19.04        10.06        36.95        37.02        17.03        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
        0.00        36.03         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03         2.01        16.08        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       24.00        27.02        13.94        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K 
       17.03        21.99         1.02        10.98        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
        1.02        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        0.92        41.00         0.07        21.37        15.52         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
       22.42        27.42         0.20        16.44         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       16.31        21.44        17.26        18.84       109.28         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.61        12.69         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.07        10.06        14.30       148.01        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       51.32         9.99         1.91        20.02        37.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02         2.96        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       13.02        11.08        10.06        12.26        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 
      119.70        24.43        38.20       130.65        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32         6.12        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        31.96        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       34.42        16.24         8.35        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       35.93        36.00        26.43        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       10.98        15.65        16.80        29.46        32.98         8.42 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 
       13.55        34.49        37.74        10.39        20.02        10.39 
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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        6.05         0.99        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99        19.04         1.02        36.95        17.03 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00H 
       14.04         1.02        17.03         3.98        46.03        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        37.02        15.95         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       70.03        64.01        51.98         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.04        38.56         1.45         0.69         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         9.37         4.73        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 
       24.13        32.61         0.49         2.40        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       16.34        16.31        11.51        10.78        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       49.51        28.57         0.39        32.19         0.53         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 10(8Q24.21) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
        4.80        46.65        42.90        42.28        44.91        37.05 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       14.53        30.44        33.53        22.09        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       24.92        61.84         7.04         3.02        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 
       13.02        38.99         1.02         9.07        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 
       19.07        34.03        21.01        17.95        29.95        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       13.94        61.02         2.01         0.92        47.05        11.01 
TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.00        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00        32.05        31.07        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       26.01        24.00         2.01        21.99        50.99        13.05 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07         7.96        27.02        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       14.99        34.98        15.02        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02        35.01        33.04        35.01        26.01        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       39.98        22.03        39.98        18.05        40.96        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 
        0.79         0.72        10.88         0.46        14.50         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       33.01        17.82        17.85        19.33        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        1.41         6.77       100.01         3.25        12.20        12.76 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       17.56        85.45        70.16        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 
       23.05        26.04        22.03        12.00        16.04        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 
       12.03        45.40        20.42        17.75        18.25        17.85 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 
        3.68         9.44        11.64         1.51        12.00        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 
       14.04        26.47        81.37       119.93        95.18        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        41.42        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 
       47.41        35.31       133.18        28.21        82.39        85.48 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       61.91        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       91.79        79.69        19.33        19.33         9.93        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2693 
       17.85        42.77        31.30        21.90        11.90        19.10 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
       14.50        16.83        15.39        11.84        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 
        7.07        20.05        34.03        12.03        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       13.94        20.98        29.98         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       13.02        35.01        14.01        20.98        13.94         6.02 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6897 
       36.03        12.00        10.98        49.97        38.96        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 
        1.81        33.17         6.97        12.39        15.02        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 
        5.95         5.29       129.27        51.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       20.91        18.28        17.69        16.41         8.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       11.97         8.45        31.30         0.66         0.69         1.12 

  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                             0                              0 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                        148.01                         139.17 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                        20.190                         19.975 
[1] "0.0 - 148.0 (20.2)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.3"
D10V2, continuous
D10V3, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   258 107
  AMP PEAK 10(8Q24.21) WILD-TYPE 188  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    258  107
  AMP PEAK 10(8Q24.21) WILD-TYPE  188   55
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON                           258                            188
  RECTUM                          107                             55
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(8Q24.21) MUTATED        56        0       24        98         4
  AMP PEAK 10(8Q24.21) WILD-TYPE      48        1       12        75         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(8Q24.21) MUTATED           3        13         13         49
  AMP PEAK 10(8Q24.21) WILD-TYPE         0        13          5         34
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(8Q24.21) MUTATED           34       48        16         0
  AMP PEAK 10(8Q24.21) WILD-TYPE         20       15        10         2
D10V4, multiclass
            clus
vv           AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  STAGE I                              56                             48
  STAGE IA                              0                              1
  STAGE II                             24                             12
  STAGE IIA                            98                             75
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            13                             13
  STAGE IIIA                           13                              5
  STAGE IIIB                           49                             34
  STAGE IIIC                           34                             20
  STAGE IV                             48                             15
  STAGE IVA                            16                             10
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 10(8Q24.21) MUTATED     8  63 256  38
  AMP PEAK 10(8Q24.21) WILD-TYPE  12  43 161  29
D10V5, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  T1                            8                             12
  T2                           63                             43
  T3                          256                            161
  T4                           38                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 10(8Q24.21) MUTATED   200  86  78
  AMP PEAK 10(8Q24.21) WILD-TYPE 145  64  37
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  N0                          200                            145
  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"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   258  64
  AMP PEAK 10(8Q24.21) WILD-TYPE 192  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    258   64
  AMP PEAK 10(8Q24.21) WILD-TYPE  192   24
   clus
vv  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  0                          258                            192
  1                           64                             24
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   164 202
  AMP PEAK 10(8Q24.21) WILD-TYPE 123 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    164  202
  AMP PEAK 10(8Q24.21) WILD-TYPE  123  123
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  FEMALE                          164                            123
  MALE                            202                            123
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   259  18
  AMP PEAK 10(8Q24.21) WILD-TYPE 187  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    259   18
  AMP PEAK 10(8Q24.21) WILD-TYPE  187   10
     clus
vv    AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  NO                           259                            187
  YES                           18                             10
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                    228
  AMP PEAK 10(8Q24.21) WILD-TYPE                  154
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                              28
  AMP PEAK 10(8Q24.21) WILD-TYPE                            32
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                     100
  AMP PEAK 10(8Q24.21) WILD-TYPE                    46
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                                5
  AMP PEAK 10(8Q24.21) WILD-TYPE                              8
D10V10, multiclass
                                clus
vv                               AMP PEAK 10(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                    228
  COLON MUCINOUS ADENOCARCINOMA                            28
  RECTAL ADENOCARCINOMA                                   100
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      154
  COLON MUCINOUS ADENOCARCINOMA                              32
  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 10(8Q24.21) MUTATED   255   3  28  19
  AMP PEAK 10(8Q24.21) WILD-TYPE 187   2   9  10
D10V11, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  R0                          255                            187
  R1                            3                              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"
D10V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(8Q24.21) MUTATED                                  0     7
  AMP PEAK 10(8Q24.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8Q24.21) MUTATED                          38   184
  AMP PEAK 10(8Q24.21) WILD-TYPE                        26   108
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  38
  WHITE                                                     184
                                  clus
vv                                 AMP PEAK 10(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED     3 215
  AMP PEAK 10(8Q24.21) WILD-TYPE   2 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED      3  215
  AMP PEAK 10(8Q24.21) WILD-TYPE    2  133
                        clus
vv                       AMP PEAK 10(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          215
                        clus
vv                       AMP PEAK 10(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(10Q22.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(10Q22.3) MUTATED    29   9
  AMP PEAK 11(10Q22.3) WILD-TYPE 443 112
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            38                            555 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                             9                            112 
$`AMP PEAK 11(10Q22.3) MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-6649 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 
       12.66         1.61        24.16         2.01        33.07        27.02 
TCGA-AA-3952 TCGA-AA-3982 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AY-A54L TCGA-CM-5860 
        2.01        27.02         1.02        35.01        17.26        32.02 
TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D7 
        2.96        11.01        19.59         4.41        14.30        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 TCGA-G4-6299 
       12.59       140.38         7.50       131.51         6.12        74.56 
TCGA-G4-6314 TCGA-G4-6317 TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-A56K TCGA-AG-3587 
       35.93        36.00        21.90        39.48        86.63        46.03 
TCGA-AG-3598 TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-A01W TCGA-AG-A020 TCGA-BM-6198 
       50.04        19.04        28.04        70.03        10.98        10.19 
TCGA-CI-6619 TCGA-DC-4745 
        6.05        21.01 

$`AMP PEAK 11(10Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       15.62         4.80         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       43.76        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-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-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        38.07         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       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-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
       15.58         1.48         3.68        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        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        16.24 
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-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       61.91        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        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-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       31.30        30.28        11.90        70.03        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       14.50        16.83        15.39        20.02        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        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-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        31.00        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        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         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        1.81        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                          1.02                           0.00 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                        140.38                         148.01 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                         20.30                          19.99 
[1] "1.0 - 140.4 (20.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    29  11
  AMP PEAK 11(10Q22.3) WILD-TYPE 417 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     29   11
  AMP PEAK 11(10Q22.3) WILD-TYPE  417  151
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON                            29                            417
  RECTUM                           11                            151
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(10Q22.3) MUTATED         5        0        2         9         0
  AMP PEAK 11(10Q22.3) WILD-TYPE      99        1       34       164        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(10Q22.3) MUTATED           0         4          2          4
  AMP PEAK 11(10Q22.3) WILD-TYPE         3        22         16         79
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(10Q22.3) MUTATED            6        6         1         0
  AMP PEAK 11(10Q22.3) WILD-TYPE         48       57        25         2
D11V4, multiclass
            clus
vv           AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              2                             34
  STAGE IIA                             9                            164
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            2                             16
  STAGE IIIB                            4                             79
  STAGE IIIC                            6                             48
  STAGE IV                              6                             57
  STAGE IVA                             1                             25
  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(10Q22.3) MUTATED     1   4  33   2
  AMP PEAK 11(10Q22.3) WILD-TYPE  19 102 384  65
D11V5, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  T1                            1                             19
  T2                            4                            102
  T3                           33                            384
  T4                            2                             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
  AMP PEAK 11(10Q22.3) MUTATED    17  11  12
  AMP PEAK 11(10Q22.3) WILD-TYPE 328 139 103
D11V6, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  N0                           17                            328
  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"
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    27   7
  AMP PEAK 11(10Q22.3) WILD-TYPE 423  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     27    7
  AMP PEAK 11(10Q22.3) WILD-TYPE  423   81
   clus
vv  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  0                           27                            423
  1                            7                             81
[1] 2 2
[1] FALSE
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    17  23
  AMP PEAK 11(10Q22.3) WILD-TYPE 270 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     17   23
  AMP PEAK 11(10Q22.3) WILD-TYPE  270  302
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  FEMALE                           17                            270
  MALE                             23                            302
[1] 2 2
[1] FALSE
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    22   3
  AMP PEAK 11(10Q22.3) WILD-TYPE 424  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     22    3
  AMP PEAK 11(10Q22.3) WILD-TYPE  424   25
     clus
vv    AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  NO                            22                            424
  YES                            3                             25
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                     24
  AMP PEAK 11(10Q22.3) WILD-TYPE                  358
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                               4
  AMP PEAK 11(10Q22.3) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                       9
  AMP PEAK 11(10Q22.3) WILD-TYPE                   137
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                                1
  AMP PEAK 11(10Q22.3) WILD-TYPE                             12
D11V10, multiclass
                                clus
vv                               AMP PEAK 11(10Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     24
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      358
  COLON MUCINOUS ADENOCARCINOMA                              56
  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 11(10Q22.3) MUTATED    27   0   1   1
  AMP PEAK 11(10Q22.3) WILD-TYPE 415   5  36  28
D11V11, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  R0                           27                            415
  R1                            0                              5
  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"
D11V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(10Q22.3) MUTATED                                  0     0
  AMP PEAK 11(10Q22.3) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(10Q22.3) MUTATED                           5    21
  AMP PEAK 11(10Q22.3) WILD-TYPE                        59   271
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(10Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      21
                                  clus
vv                                 AMP PEAK 11(10Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    59
  WHITE                                                       271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED     1  23
  AMP PEAK 11(10Q22.3) WILD-TYPE   4 325
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED      1   23
  AMP PEAK 11(10Q22.3) WILD-TYPE    4  325
                        clus
vv                       AMP PEAK 11(10Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       AMP PEAK 11(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            325
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(11P15.5) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(11P15.5) MUTATED   105  28
  AMP PEAK 12(11P15.5) WILD-TYPE 367  93
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           133                            460 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                            28                             93 
$`AMP PEAK 12(11P15.5) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
       43.76        43.43        24.33        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3506 
       25.18        23.87         9.63         5.03         1.02        58.03 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        9.07        24.03         0.00        19.07        34.03        29.00 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 
       12.99        13.02        24.00        23.01        13.94        19.99 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 
       50.04        47.01         5.03        25.02        17.98        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 
       17.03        33.07         0.99        24.03        18.05        20.98 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01D 
       27.02        19.07        34.03        17.03        21.99        10.98 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6888 
        1.02        35.01        26.01        39.98         5.03        15.52 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 
       22.42         0.46        16.31         0.95        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 
       62.79        29.56         3.19         1.61         2.14         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 
       12.20        14.30       148.01         8.02        30.08        17.03 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 
       29.03        21.99        11.08        12.26        56.09         1.32 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G 
       17.85         1.48         4.80        49.91        35.97        60.79 
TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 
       31.96        35.74         8.35        74.56        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6314 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2689 
       63.62        35.93        42.77        29.46        30.28        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       17.23        13.55        10.39        16.83        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3587 
       65.98        36.03        12.00         8.02        20.05        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       34.03        34.03        34.03        19.99        13.94        19.99 
TCGA-AG-3727 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N 
        0.99        14.01        36.03         1.02        25.97        31.00 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 
       26.43        10.19         9.37        12.39        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5830 
        5.03         8.98        27.95        19.99       126.44         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 
        2.40        20.55        16.31         0.39        32.19         1.12 
TCGA-G5-6233 
       18.28 

$`AMP PEAK 12(11P15.5) WILD-TYPE`
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-A6-2681 
       46.65        43.76        42.90        42.28        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
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-A6-6649 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        56.25         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       19.07        29.00        26.01         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       21.01        17.95        29.95        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        47.05        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00        85.05        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       36.95        14.93         0.00        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        24.00         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         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         1.02 
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-A01T TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        33.04        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.96         2.01         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         5.79        27.42        10.88         0.20        16.44 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74        12.69         3.06         3.25         3.29        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       10.06        17.56        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       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-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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00         2.96 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        14.99        12.99        13.02        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-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        19.59        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         3.68         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       47.41        35.31       133.18        28.21        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       67.30        53.62        44.68        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        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-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       17.85        16.80        32.98         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       11.90        70.03        24.13        43.04        19.10        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3578 
       37.74        14.50        15.39        86.63        11.84        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        7.07        36.03        24.00         1.02         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-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 
       38.56         1.45         0.69         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       33.17         6.97         4.73        78.12         7.17        21.01 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        10.98         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       32.61        19.96        20.91        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-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-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 
       31.30        28.57         0.66         0.69         0.53         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        55.76        47.08        26.43 

  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                             0                              0 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                         19.99                          19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    90  44
  AMP PEAK 12(11P15.5) WILD-TYPE 356 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     90   44
  AMP PEAK 12(11P15.5) WILD-TYPE  356  118
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  COLON                            90                            356
  RECTUM                           44                            118
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(11P15.5) MUTATED        20        0        6        35         2
  AMP PEAK 12(11P15.5) WILD-TYPE      84        1       30       138         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(11P15.5) MUTATED           1         7          6         17
  AMP PEAK 12(11P15.5) WILD-TYPE         2        19         12         66
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(11P15.5) MUTATED           15       18         7         0
  AMP PEAK 12(11P15.5) WILD-TYPE         39       45        19         2
D12V4, multiclass
            clus
vv           AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            35                            138
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                            6                             12
  STAGE IIIB                           17                             66
  STAGE IIIC                           15                             39
  STAGE IV                             18                             45
  STAGE IVA                             7                             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
  AMP PEAK 12(11P15.5) MUTATED     6  23  98   9
  AMP PEAK 12(11P15.5) WILD-TYPE  14  83 319  58
D12V5, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  T1                            6                             14
  T2                           23                             83
  T3                           98                            319
  T4                            9                             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
  AMP PEAK 12(11P15.5) MUTATED    70  35  31
  AMP PEAK 12(11P15.5) WILD-TYPE 275 115  84
D12V6, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  N0                           70                            275
  N1                           35                            115
  N2                           31                             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    99  24
  AMP PEAK 12(11P15.5) WILD-TYPE 351  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     99   24
  AMP PEAK 12(11P15.5) WILD-TYPE  351   64
   clus
vv  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  0                           99                            351
  1                           24                             64
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    66  70
  AMP PEAK 12(11P15.5) WILD-TYPE 221 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     66   70
  AMP PEAK 12(11P15.5) WILD-TYPE  221  255
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  FEMALE                           66                            221
  MALE                             70                            255
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    98   8
  AMP PEAK 12(11P15.5) WILD-TYPE 348  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     98    8
  AMP PEAK 12(11P15.5) WILD-TYPE  348   20
     clus
vv    AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  NO                            98                            348
  YES                            8                             20
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                     85
  AMP PEAK 12(11P15.5) WILD-TYPE                  297
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                               4
  AMP PEAK 12(11P15.5) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                      43
  AMP PEAK 12(11P15.5) WILD-TYPE                   103
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                                1
  AMP PEAK 12(11P15.5) WILD-TYPE                             12
D12V10, multiclass
                                clus
vv                               AMP PEAK 12(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                     85
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 12(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                      297
  COLON MUCINOUS ADENOCARCINOMA                              56
  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 12(11P15.5) MUTATED    97   1  10   7
  AMP PEAK 12(11P15.5) WILD-TYPE 345   4  27  22
D12V11, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  R0                           97                            345
  R1                            1                              4
  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"
D12V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(11P15.5) MUTATED                                  0     4
  AMP PEAK 12(11P15.5) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(11P15.5) MUTATED                          11    64
  AMP PEAK 12(11P15.5) WILD-TYPE                        53   228
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      64
                                  clus
vv                                 AMP PEAK 12(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    53
  WHITE                                                       228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED     1  76
  AMP PEAK 12(11P15.5) WILD-TYPE   4 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED      1   76
  AMP PEAK 12(11P15.5) WILD-TYPE    4  272
                        clus
vv                       AMP PEAK 12(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       AMP PEAK 12(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            272
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(12P13.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(12P13.32) MUTATED   111  32
  AMP PEAK 13(12P13.32) WILD-TYPE 361  89
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            143                             450 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             32                              89 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 
       15.62        12.66        44.91        13.94        37.02        34.65 
TCGA-A6-4105 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 
       14.53        22.09        25.08        20.61        20.12        20.28 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3532 
       24.92         1.02        58.03        36.03         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 
       29.00        12.99        19.99        78.08         0.92        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 
        0.99        37.02        14.93         0.00        33.07         0.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A00F 
       12.99        24.00        26.01        24.00         2.01        34.03 
TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O 
       18.05        12.00        31.00        33.04        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6965 
       22.03        39.98        40.96         0.07        27.42         0.20 
TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 
        0.92        18.84         1.41         5.13        49.41         6.77 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 
       11.74         3.19         1.61         3.06       148.01        85.45 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 
       15.62        51.32        20.02        25.02        30.08        32.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       15.02        15.02        21.99        13.02        14.04        11.01 
TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 
       11.01        20.19        17.75         4.80        12.49        15.58 
TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30        11.64         4.80        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 
       24.43        13.32        44.32        95.18         8.61        47.87 
TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U 
       34.42        44.68        35.93        13.78        74.79        10.98 
TCGA-NH-A6GB TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       15.65        21.90        19.10        34.49        37.74        14.50 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 
       16.83        10.39        36.03        46.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3883 
       19.99        13.94         7.99        37.02        19.04         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 
       36.95         1.02        36.03        46.03        15.95        36.03 
TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 
       38.96        61.97         4.73        78.12         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
        5.29       126.44        32.61        19.96        18.28        17.69 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6812 TCGA-G5-6233 TCGA-G5-6641 
       13.64        11.97         0.66        18.28        26.43 

$`AMP PEAK 13(12P13.32) WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       43.76        43.43        42.90        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3810 TCGA-A6-4107 
       45.60        16.57        37.05        37.25        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       23.87        19.66        16.24        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        5.03         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        37.05         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       34.03        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 
       19.00        36.00        85.05        19.04        10.06        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        36.95        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       10.06         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 
       18.05        31.00         2.01        33.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        26.01        37.02        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 
        2.01         5.03        41.00        18.05        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        22.42        10.88 
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-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-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
      109.28        75.95        58.39         5.65        32.94       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        65.00        62.79        88.21        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        12.69         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        49.08         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       14.99        12.99        15.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       15.12        17.85        17.13        16.14         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 
        4.41        12.43         9.04         9.44         1.51        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        79.69        18.18        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30        30.28        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-6136 
       39.48        17.23        43.04        13.55        10.39        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       20.02        86.63        65.98        11.84        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
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-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99        20.98         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        17.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 
       33.17         6.97         9.37        12.39         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD 
       27.95        10.98        19.99         5.95        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
       49.51        31.30        28.57         0.39        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        12.46        55.76        47.08 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                              0                               0 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         18.840                          20.945 
[1] "0.0 - 148.0 (18.8)" "0.0 - 140.4 (20.9)"
[1] "hr=" "1.3"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   110  38
  AMP PEAK 13(12P13.32) WILD-TYPE 336 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    110   38
  AMP PEAK 13(12P13.32) WILD-TYPE  336  124
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  COLON                            110                             336
  RECTUM                            38                             124
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(12P13.32) MUTATED        23        1       13        50         2
  AMP PEAK 13(12P13.32) WILD-TYPE      81        0       23       123         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(12P13.32) MUTATED           1         5          5         10
  AMP PEAK 13(12P13.32) WILD-TYPE         2        21         13         73
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(12P13.32) MUTATED           15       15         8         0
  AMP PEAK 13(12P13.32) WILD-TYPE         39       48        18         2
D13V4, multiclass
            clus
vv           AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  STAGE I                               23                              81
  STAGE IA                               1                               0
  STAGE II                              13                              23
  STAGE IIA                             50                             123
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              5                              21
  STAGE IIIA                             5                              13
  STAGE IIIB                            10                              73
  STAGE IIIC                            15                              39
  STAGE IV                              15                              48
  STAGE IVA                              8                              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 13(12P13.32) MUTATED     2  28 100  19
  AMP PEAK 13(12P13.32) WILD-TYPE  18  78 317  48
D13V5, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  T1                             2                              18
  T2                            28                              78
  T3                           100                             317
  T4                            19                              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 13(12P13.32) MUTATED    94  27  29
  AMP PEAK 13(12P13.32) WILD-TYPE 251 123  86
D13V6, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  N0                            94                             251
  N1                            27                             123
  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"
D13V7, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   107  20
  AMP PEAK 13(12P13.32) WILD-TYPE 343  68
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    107   20
  AMP PEAK 13(12P13.32) WILD-TYPE  343   68
   clus
vv  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  0                           107                             343
  1                            20                              68
[1] 2 2
[1] FALSE
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    69  81
  AMP PEAK 13(12P13.32) WILD-TYPE 218 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     69   81
  AMP PEAK 13(12P13.32) WILD-TYPE  218  244
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            69                             218
  MALE                              81                             244
[1] 2 2
[1] FALSE
D13V9, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   105   9
  AMP PEAK 13(12P13.32) WILD-TYPE 341  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    105    9
  AMP PEAK 13(12P13.32) WILD-TYPE  341   19
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                            105                             341
  YES                             9                              19
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                     96
  AMP PEAK 13(12P13.32) WILD-TYPE                  286
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                              13
  AMP PEAK 13(12P13.32) WILD-TYPE                            47
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                      32
  AMP PEAK 13(12P13.32) WILD-TYPE                   114
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                                5
  AMP PEAK 13(12P13.32) WILD-TYPE                              8
D13V10, multiclass
                                clus
vv                               AMP PEAK 13(12P13.32) MUTATED
  COLON ADENOCARCINOMA                                      96
  COLON MUCINOUS ADENOCARCINOMA                             13
  RECTAL ADENOCARCINOMA                                     32
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 13(12P13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       286
  COLON MUCINOUS ADENOCARCINOMA                               47
  RECTAL ADENOCARCINOMA                                      114
  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(12P13.32) MUTATED   109   1   6   6
  AMP PEAK 13(12P13.32) WILD-TYPE 333   4  31  23
D13V11, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  R0                           109                             333
  R1                             1                               4
  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"
D13V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(12P13.32) MUTATED                                  0     2
  AMP PEAK 13(12P13.32) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(12P13.32) MUTATED                          12    74
  AMP PEAK 13(12P13.32) WILD-TYPE                        52   218
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       74
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     52
  WHITE                                                        218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     0  85
  AMP PEAK 13(12P13.32) WILD-TYPE   5 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      0   85
  AMP PEAK 13(12P13.32) WILD-TYPE    5  263
                        clus
vv                       AMP PEAK 13(12P13.32) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            85
                        clus
vv                       AMP PEAK 13(12P13.32) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             263
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(13Q12.13) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 14(13Q12.13) MUTATED   309  78
  AMP PEAK 14(13Q12.13) WILD-TYPE 163  43
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            387                             206 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                             78                              43 
$`AMP PEAK 14(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       45.60        13.94        16.57        34.65        36.53        14.53 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.18        24.16        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-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       37.05         1.02        58.03         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       24.03        36.03        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       24.00        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 
        6.05         2.01        14.01        50.04        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 
       37.05        19.00         5.03        85.05        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       35.05         0.99        25.02        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03        10.06        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 
       17.03        24.03        27.02        29.98         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       38.04        42.02        14.99         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F 
       32.02        12.00        31.00        33.04         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 
        2.01        41.00        39.98        40.96        21.37         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        5.79        22.42        27.42         0.20        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        33.01        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
      109.28        75.95         1.41         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 
       11.74         1.61        12.69         3.06         0.07        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       17.56       148.01        49.08         9.99         1.91        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02         5.03        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
        2.96        29.03        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 
       12.26        19.59        56.09        55.92        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
        4.80        12.00        11.38        10.26       119.70       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-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 
        6.12        14.04        26.47       119.93        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96         6.18        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       23.51        74.56        65.85        44.68        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.00        26.43        35.80        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       74.79        18.18        19.33        15.65        17.85        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        30.28 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 
       20.02        10.39        86.63        65.98        11.84         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       34.03         2.01         0.99        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       20.98         0.99        29.98         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         3.98        46.03         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 
       37.02        15.95        36.03         9.07        12.00        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97         1.94        38.96        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02         5.03         8.98        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        10.78        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        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       32.19         0.66         0.69         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`AMP PEAK 14(13Q12.13) WILD-TYPE`
TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
        1.61        42.90        24.33        37.05        37.25        37.02 
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-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 
       63.98         1.02        13.02         1.02        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       19.07         0.00        19.07        17.95        29.95        23.01 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       61.02         6.97        54.02         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3831 
       11.01        36.00        26.99        19.04         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-3950 
       36.03        53.00        18.05        31.00        33.01        24.00 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        2.01         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-A00Z 
       18.05         4.01        27.02         0.99        17.03        21.99 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       34.98        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J 
       35.01        26.01        37.02        39.06        51.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
        0.92        22.03        18.05         0.07        15.52        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6386 
        0.72        10.88         0.46         0.92        27.09        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-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01         3.19         2.14         3.25         3.29 
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         3.68         9.44        11.64 
TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
        1.51        24.43        38.20        12.59       140.38        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65       139.17        81.37        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       95.18        11.11        35.74        35.74        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       34.42        35.31        67.30        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 
       61.91        22.09        26.04        13.78        26.17        79.69 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 
       10.98        19.33         9.93        12.79        31.30        70.03 
TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 
       34.49        36.03        12.00        32.02         8.02        24.00 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 
       50.04        12.03         6.05        15.95         7.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
       32.98         0.99        19.04        13.02        48.03        20.98 
TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       13.94         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-DC-6155 
       61.97        41.00         1.45         1.81        10.19        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
        5.95         5.29        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.12 

  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                         19.990                          20.305 
[1] "0.1 - 148.0 (20.0)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   272 123
  AMP PEAK 14(13Q12.13) WILD-TYPE 174  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    272  123
  AMP PEAK 14(13Q12.13) WILD-TYPE  174   39
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  COLON                            272                             174
  RECTUM                           123                              39
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(13Q12.13) MUTATED        64        0       16       100         4
  AMP PEAK 14(13Q12.13) WILD-TYPE      40        1       20        73         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(13Q12.13) MUTATED           3        16         15         62
  AMP PEAK 14(13Q12.13) WILD-TYPE         0        10          3         21
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(13Q12.13) MUTATED           38       51        22         0
  AMP PEAK 14(13Q12.13) WILD-TYPE         16       12         4         2
D14V4, multiclass
            clus
vv           AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  STAGE I                               64                              40
  STAGE IA                               0                               1
  STAGE II                              16                              20
  STAGE IIA                            100                              73
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             16                              10
  STAGE IIIA                            15                               3
  STAGE IIIB                            62                              21
  STAGE IIIC                            38                              16
  STAGE IV                              51                              12
  STAGE IVA                             22                               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 14(13Q12.13) MUTATED    14  65 274  45
  AMP PEAK 14(13Q12.13) WILD-TYPE   6  41 143  22
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  T1                            14                               6
  T2                            65                              41
  T3                           274                             143
  T4                            45                              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 14(13Q12.13) MUTATED   197 113  87
  AMP PEAK 14(13Q12.13) WILD-TYPE 148  37  28
D14V6, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  N0                           197                             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"
D14V7, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   282  70
  AMP PEAK 14(13Q12.13) WILD-TYPE 168  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    282   70
  AMP PEAK 14(13Q12.13) WILD-TYPE  168   18
   clus
vv  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  0                           282                             168
  1                            70                              18
[1] 2 2
[1] FALSE
D14V8, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   184 215
  AMP PEAK 14(13Q12.13) WILD-TYPE 103 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    184  215
  AMP PEAK 14(13Q12.13) WILD-TYPE  103  110
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  FEMALE                           184                             103
  MALE                             215                             110
[1] 2 2
[1] FALSE
D14V9, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   298  22
  AMP PEAK 14(13Q12.13) WILD-TYPE 148   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    298   22
  AMP PEAK 14(13Q12.13) WILD-TYPE  148    6
     clus
vv    AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  NO                            298                             148
  YES                            22                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                    253
  AMP PEAK 14(13Q12.13) WILD-TYPE                  129
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                              18
  AMP PEAK 14(13Q12.13) WILD-TYPE                            42
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                     117
  AMP PEAK 14(13Q12.13) WILD-TYPE                    29
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                                5
  AMP PEAK 14(13Q12.13) WILD-TYPE                              8
D14V10, multiclass
                                clus
vv                               AMP PEAK 14(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                     253
  COLON MUCINOUS ADENOCARCINOMA                             18
  RECTAL ADENOCARCINOMA                                    117
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 14(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                       129
  COLON MUCINOUS ADENOCARCINOMA                               42
  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 14(13Q12.13) MUTATED   283   3  29  13
  AMP PEAK 14(13Q12.13) WILD-TYPE 159   2   8  16
D14V11, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  R0                           283                             159
  R1                             3                               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"
D14V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(13Q12.13) MUTATED                                  0     4
  AMP PEAK 14(13Q12.13) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(13Q12.13) MUTATED                          42   204
  AMP PEAK 14(13Q12.13) WILD-TYPE                        22    88
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      204
                                  clus
vv                                 AMP PEAK 14(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                         88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED     4 235
  AMP PEAK 14(13Q12.13) WILD-TYPE   1 113
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED      4  235
  AMP PEAK 14(13Q12.13) WILD-TYPE    1  113
                        clus
vv                       AMP PEAK 14(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           235
                        clus
vv                       AMP PEAK 14(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             113
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q12.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(13Q12.2) MUTATED   306  76
  AMP PEAK 15(13Q12.2) WILD-TYPE 166  45
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           382                            211 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                            76                             45 
$`AMP PEAK 15(13Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       45.60        13.94        16.57        34.65        36.53        14.53 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.18        24.16        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-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       37.05         1.02        58.03         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       24.03        36.03        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       24.00        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 
        6.05         2.01        14.01        50.04        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       37.05        19.00        85.05        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99        36.95        37.02        14.93        17.03        10.06 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       27.02        29.98         2.01        12.99        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       34.06        26.01        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W 
       13.94        19.00        34.03        38.04        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y 
       33.04         2.96        39.98         2.01        41.00        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        21.37         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 
       21.44        17.26        18.84       109.28        75.95         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13       106.75        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        3.06         0.07        14.30        17.56       148.01        49.08 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        9.99         1.91        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         2.96        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        12.26        19.59        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         1.32        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         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04         4.80        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        7.50       131.51         7.76         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 
      119.93        35.97         8.61        31.96         6.18        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 
       28.21         8.35        82.39        23.51        65.85        44.68 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 
       63.62        39.42        35.93        36.00        26.43        35.80 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       91.79        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        30.28        11.90        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        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-3611 
       34.03        34.03         2.01         0.99        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       19.99        20.98         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
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-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         3.98        46.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.97         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-6622 
       38.56         0.69         0.72        26.43         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02         5.03         8.98        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        19.99         4.01         5.03       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        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-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39        32.19         0.66         0.69         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK 15(13Q12.2) WILD-TYPE`
TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
        1.61        42.90        24.33        37.05        37.25        37.02 
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-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 
       63.98         1.02        13.02         1.02        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       19.07         0.00        19.07        17.95        29.95        23.01 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       61.02         6.97        54.02         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 
       11.01        36.00         5.03        26.99        19.04        25.02 
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-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 
       33.01        24.00         2.01         2.01        25.02        24.00 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P 
        0.99        17.03        21.99        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        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F 
       39.06        51.98         5.03         0.92        22.03        18.05 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
        0.07        15.52        56.55         0.72        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
        0.92        27.09        17.82        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 
        5.65        32.94        88.21         6.77       100.01         3.19 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29        12.20        12.76        10.06 
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-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        27.02        15.02 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       15.02        12.00        21.99        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.03        45.40        20.19        20.42        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF 
        3.68         9.44        11.64         1.51        24.43        38.20 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38        44.32       135.65       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 
       35.74        47.87         1.55        34.42        35.31        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       67.30        53.62        55.04        85.48        61.91        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        26.17        79.69        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 
        9.93        12.79        31.30        70.03        34.49        16.83 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3598 
       36.03        12.00        32.02         8.02        24.00        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       12.03         6.05        15.95         7.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 
        0.99        19.04        13.02        48.03        20.98        13.94 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N 
        1.02        31.00        70.03        64.01        10.98        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 
        1.45         1.81        10.19        33.17        13.97         5.95 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 
        5.29        19.96         8.61        13.64        17.46         0.53 
TCGA-F5-6861 
        1.12 

  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                         19.99                          20.42 
[1] "0.1 - 148.0 (20.0)" "0.0 - 140.4 (20.4)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   268 122
  AMP PEAK 15(13Q12.2) WILD-TYPE 178  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    268  122
  AMP PEAK 15(13Q12.2) WILD-TYPE  178   40
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  COLON                           268                            178
  RECTUM                          122                             40
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(13Q12.2) MUTATED        64        0       16        98         4
  AMP PEAK 15(13Q12.2) WILD-TYPE      40        1       20        75         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(13Q12.2) MUTATED           3        16         15         62
  AMP PEAK 15(13Q12.2) WILD-TYPE         0        10          3         21
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(13Q12.2) MUTATED           37       50        21         0
  AMP PEAK 15(13Q12.2) WILD-TYPE         17       13         5         2
D15V4, multiclass
            clus
vv           AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  STAGE I                              64                             40
  STAGE IA                              0                              1
  STAGE II                             16                             20
  STAGE IIA                            98                             75
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           15                              3
  STAGE IIIB                           62                             21
  STAGE IIIC                           37                             17
  STAGE IV                             50                             13
  STAGE IVA                            21                              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 15(13Q12.2) MUTATED    14  65 269  45
  AMP PEAK 15(13Q12.2) WILD-TYPE   6  41 148  22
D15V5, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  T1                           14                              6
  T2                           65                             41
  T3                          269                            148
  T4                           45                             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 15(13Q12.2) MUTATED   195 111  86
  AMP PEAK 15(13Q12.2) WILD-TYPE 150  39  29
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  N0                          195                            150
  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"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   279  68
  AMP PEAK 15(13Q12.2) WILD-TYPE 171  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    279   68
  AMP PEAK 15(13Q12.2) WILD-TYPE  171   20
   clus
vv  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  0                          279                            171
  1                           68                             20
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   180 214
  AMP PEAK 15(13Q12.2) WILD-TYPE 107 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    180  214
  AMP PEAK 15(13Q12.2) WILD-TYPE  107  111
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  FEMALE                          180                            107
  MALE                            214                            111
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   292  22
  AMP PEAK 15(13Q12.2) WILD-TYPE 154   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    292   22
  AMP PEAK 15(13Q12.2) WILD-TYPE  154    6
     clus
vv    AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  NO                           292                            154
  YES                           22                              6
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                    249
  AMP PEAK 15(13Q12.2) WILD-TYPE                  133
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                              18
  AMP PEAK 15(13Q12.2) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                     116
  AMP PEAK 15(13Q12.2) WILD-TYPE                    30
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                                5
  AMP PEAK 15(13Q12.2) WILD-TYPE                              8
D15V10, multiclass
                                clus
vv                               AMP PEAK 15(13Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    249
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                   116
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 15(13Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      133
  COLON MUCINOUS ADENOCARCINOMA                              42
  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 15(13Q12.2) MUTATED   280   3  28  13
  AMP PEAK 15(13Q12.2) WILD-TYPE 162   2   9  16
D15V11, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  R0                          280                            162
  R1                            3                              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"
D15V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q12.2) MUTATED                                  0     4
  AMP PEAK 15(13Q12.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q12.2) MUTATED                          42   201
  AMP PEAK 15(13Q12.2) WILD-TYPE                        22    91
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  42
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 15(13Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                        91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED     4 232
  AMP PEAK 15(13Q12.2) WILD-TYPE   1 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED      4  232
  AMP PEAK 15(13Q12.2) WILD-TYPE    1  116
                        clus
vv                       AMP PEAK 15(13Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          232
                        clus
vv                       AMP PEAK 15(13Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            116
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(13Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(13Q22.1) MUTATED   306  78
  AMP PEAK 16(13Q22.1) WILD-TYPE 166  43
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           384                            209 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            78                             43 
$`AMP PEAK 16(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       45.60        13.94        16.57        34.65        36.53        14.53 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.18        24.16        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-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       37.05         1.02        58.03         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       24.03        36.03        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 
       54.02         2.01        14.01        50.04        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       37.05        19.00        85.05        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99        36.95        37.02        14.93        17.03        10.06 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05         2.01        12.99        24.00        26.01 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       13.05        34.06        26.01        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       27.02        13.94        19.00        34.03        38.04        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F 
       12.00        31.00         1.02        33.04         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        2.01        41.00        39.98        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 
       21.44        17.26        18.84       109.28        75.95         1.41 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        0.07        14.30        17.56       148.01        49.08         9.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        1.91        20.02        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-5864 
       22.03        22.98        30.08        32.02         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02         2.96        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       12.99        13.02        15.02        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        10.06        12.26        19.59        56.09        55.92 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.80        17.13        12.49         1.48         4.41        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04         4.80        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-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 
       13.32         7.50       131.51         7.76         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 
       26.47       119.93        35.97        31.96         6.18        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67        13.25         0.53        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       44.68        63.62        39.42        35.93        36.00        26.43 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       35.80        91.79        46.75        74.79        18.18        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42        21.90        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        15.39        20.02        10.39        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-3611 
       34.03        34.03        34.03         0.99        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       19.99        20.98         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
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-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        46.03         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        38.96        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.69         0.72        26.43         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02         5.03         8.98        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         4.01         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-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-7002 TCGA-F5-6464 
       16.31        16.41        11.51        10.78        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76        18.28        55.76        47.08        26.43 

$`AMP PEAK 16(13Q22.1) WILD-TYPE`
TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
        1.61        42.90        24.33        37.05        37.25        37.02 
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-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 
       63.98         1.02        13.02         1.02        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 
       19.07         0.00        19.07        33.99        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       23.01        61.02         6.97         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 
       11.01        36.00         5.03        26.99        19.04        25.02 
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-3860 TCGA-AA-3864 TCGA-AA-3877 
       33.07         0.00        36.03        31.07        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A 
       33.01        24.00         2.01        25.02        24.00        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-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       21.99        34.98        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J 
       35.01        26.01        37.02        39.06        51.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 
        0.92        22.03        18.05        56.55        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
        0.92        27.09        17.82        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
        5.65        32.94       106.75        88.21         6.77       100.01 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.19         2.14         3.25         3.29        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       10.06        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
       82.95       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 
       15.02        15.02        12.00        21.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 
       13.05        12.03        45.40        20.19        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D8 
       15.58         3.68         9.44        11.64         1.51        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G 
      140.38        44.32       135.65       139.17        81.37        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 
       35.74        47.87         1.55        34.42        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        55.04        85.48        61.91        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GC 
       13.78        26.17        79.69        10.98        19.33        12.79 
TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
       31.30        11.90        70.03        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 
       12.00        32.02         8.02        24.00         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       12.03         6.05        15.95         7.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A002 
        0.99        19.04        13.02        48.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N 
       13.94        37.02         1.02        31.00        10.98        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 
       41.00         1.45         1.81        10.19        33.17        13.97 
TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 
        5.95         2.40        19.96        20.91         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       17.46         8.45         0.53         1.12        12.46 

  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                         19.99                          20.91 
[1] "0.1 - 148.0 (20.0)" "0.0 - 140.4 (20.9)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   275 117
  AMP PEAK 16(13Q22.1) WILD-TYPE 171  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    275  117
  AMP PEAK 16(13Q22.1) WILD-TYPE  171   45
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON                           275                            171
  RECTUM                          117                             45
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(13Q22.1) MUTATED        65        0       20        94         4
  AMP PEAK 16(13Q22.1) WILD-TYPE      39        1       16        79         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(13Q22.1) MUTATED           3        17         15         60
  AMP PEAK 16(13Q22.1) WILD-TYPE         0         9          3         23
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(13Q22.1) MUTATED           40       49        20         0
  AMP PEAK 16(13Q22.1) WILD-TYPE         14       14         6         2
D16V4, multiclass
            clus
vv           AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  STAGE I                              65                             39
  STAGE IA                              0                              1
  STAGE II                             20                             16
  STAGE IIA                            94                             79
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            17                              9
  STAGE IIIA                           15                              3
  STAGE IIIB                           60                             23
  STAGE IIIC                           40                             14
  STAGE IV                             49                             14
  STAGE IVA                            20                              6
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(13Q22.1) MUTATED    15  65 270  45
  AMP PEAK 16(13Q22.1) WILD-TYPE   5  41 147  22
D16V5, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  T1                           15                              5
  T2                           65                             41
  T3                          270                            147
  T4                           45                             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 16(13Q22.1) MUTATED   196 113  85
  AMP PEAK 16(13Q22.1) WILD-TYPE 149  37  30
D16V6, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  N0                          196                            149
  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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   279  67
  AMP PEAK 16(13Q22.1) WILD-TYPE 171  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    279   67
  AMP PEAK 16(13Q22.1) WILD-TYPE  171   21
   clus
vv  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  0                          279                            171
  1                           67                             21
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   178 218
  AMP PEAK 16(13Q22.1) WILD-TYPE 109 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    178  218
  AMP PEAK 16(13Q22.1) WILD-TYPE  109  107
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  FEMALE                          178                            109
  MALE                            218                            107
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   288  22
  AMP PEAK 16(13Q22.1) WILD-TYPE 158   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    288   22
  AMP PEAK 16(13Q22.1) WILD-TYPE  158    6
     clus
vv    AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  NO                           288                            158
  YES                           22                              6
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                    254
  AMP PEAK 16(13Q22.1) WILD-TYPE                  128
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                              19
  AMP PEAK 16(13Q22.1) WILD-TYPE                            41
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                     112
  AMP PEAK 16(13Q22.1) WILD-TYPE                    34
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                                4
  AMP PEAK 16(13Q22.1) WILD-TYPE                              9
D16V10, multiclass
                                clus
vv                               AMP PEAK 16(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    254
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                   112
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  COLON MUCINOUS ADENOCARCINOMA                              41
  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 16(13Q22.1) MUTATED   279   3  27  14
  AMP PEAK 16(13Q22.1) WILD-TYPE 163   2  10  15
D16V11, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  R0                          279                            163
  R1                            3                              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"
D16V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(13Q22.1) MUTATED                                  0     5
  AMP PEAK 16(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(13Q22.1) MUTATED                          42   201
  AMP PEAK 16(13Q22.1) WILD-TYPE                        22    91
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  42
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 16(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                        91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED     4 232
  AMP PEAK 16(13Q22.1) WILD-TYPE   1 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      4  232
  AMP PEAK 16(13Q22.1) WILD-TYPE    1  116
                        clus
vv                       AMP PEAK 16(13Q22.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          232
                        clus
vv                       AMP PEAK 16(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            116
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(15Q26.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q26.1) MUTATED    29  10
  AMP PEAK 17(15Q26.1) WILD-TYPE 443 111
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            39                            554 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            10                            111 
$`AMP PEAK 17(15Q26.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-6649 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3560 
       15.62        43.76        24.16        29.00        29.00        19.99 
TCGA-AA-3681 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 TCGA-AA-A02H TCGA-AY-4070 
        5.98        36.03         0.99        24.00         2.01        16.31 
TCGA-AZ-4614 TCGA-CA-5254 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-6161 TCGA-D5-6531 
        5.65        12.69        22.98        30.08        15.02        17.75 
TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-G4-6297 TCGA-G4-6299 
       17.13        44.32        14.04        26.47        82.39        74.56 
TCGA-G4-6626 TCGA-QG-A5YV TCGA-AF-3400 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3612 
       46.75        42.77        34.49        46.03        19.99        19.99 
TCGA-AG-A01W TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5918 TCGA-DY-A1DC 
       70.03         0.69        10.19         9.37         7.17        41.36 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6864 
        8.45         9.96        12.46 

$`AMP PEAK 17(15Q26.1) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       43.76        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-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-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        0.00        19.07        34.03        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
        0.00        32.05        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
        1.02        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-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20        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-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19         1.61         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
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-5341 TCGA-CM-5344 TCGA-CM-5860 
        8.02        27.02        13.02        29.06        22.03        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
        2.96        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 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
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         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        6.12        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 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
      133.18        28.21         8.35        23.51        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        74.79        79.69 
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-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        30.28        11.90        70.03        24.13 
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        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        13.94        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-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.72        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        6.97         4.73        12.39        78.12        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                          0.69                           0.00 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                         82.39                         148.01 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                        19.990                         20.005 
[1] "0.7 - 82.4 (20.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    29  13
  AMP PEAK 17(15Q26.1) WILD-TYPE 417 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     29   13
  AMP PEAK 17(15Q26.1) WILD-TYPE  417  149
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  COLON                            29                            417
  RECTUM                           13                            149
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(15Q26.1) MUTATED         5        0        1        11         0
  AMP PEAK 17(15Q26.1) WILD-TYPE      99        1       35       162        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(15Q26.1) MUTATED           0         1          0          6
  AMP PEAK 17(15Q26.1) WILD-TYPE         3        25         18         77
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(15Q26.1) MUTATED           10        5         3         0
  AMP PEAK 17(15Q26.1) WILD-TYPE         44       58        23         2
D17V4, multiclass
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            11                            162
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             1                             25
  STAGE IIIA                            0                             18
  STAGE IIIB                            6                             77
  STAGE IIIC                           10                             44
  STAGE IV                              5                             58
  STAGE IVA                             3                             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 17(15Q26.1) MUTATED     1   4  30   7
  AMP PEAK 17(15Q26.1) WILD-TYPE  19 102 387  60
D17V5, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1                            1                             19
  T2                            4                            102
  T3                           30                            387
  T4                            7                             60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 17(15Q26.1) MUTATED    17   8  17
  AMP PEAK 17(15Q26.1) WILD-TYPE 328 142  98
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  N0                           17                            328
  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"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    31   7
  AMP PEAK 17(15Q26.1) WILD-TYPE 419  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     31    7
  AMP PEAK 17(15Q26.1) WILD-TYPE  419   81
   clus
vv  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  0                           31                            419
  1                            7                             81
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    24  18
  AMP PEAK 17(15Q26.1) WILD-TYPE 263 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     24   18
  AMP PEAK 17(15Q26.1) WILD-TYPE  263  307
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  FEMALE                           24                            263
  MALE                             18                            307
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    27   3
  AMP PEAK 17(15Q26.1) WILD-TYPE 419  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     27    3
  AMP PEAK 17(15Q26.1) WILD-TYPE  419   25
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NO                            27                            419
  YES                            3                             25
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                     25
  AMP PEAK 17(15Q26.1) WILD-TYPE                  357
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                               4
  AMP PEAK 17(15Q26.1) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                      11
  AMP PEAK 17(15Q26.1) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                                2
  AMP PEAK 17(15Q26.1) WILD-TYPE                             11
D17V10, multiclass
                                clus
vv                               AMP PEAK 17(15Q26.1) MUTATED
  COLON ADENOCARCINOMA                                     25
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK 17(15Q26.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      357
  COLON MUCINOUS ADENOCARCINOMA                              56
  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 17(15Q26.1) MUTATED    30   1   3   2
  AMP PEAK 17(15Q26.1) WILD-TYPE 412   4  34  27
D17V11, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  R0                           30                            412
  R1                            1                              4
  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"
D17V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(15Q26.1) MUTATED                                  0     1
  AMP PEAK 17(15Q26.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(15Q26.1) MUTATED                           3    24
  AMP PEAK 17(15Q26.1) WILD-TYPE                        61   268
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(15Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 17(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    61
  WHITE                                                       268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED     0  27
  AMP PEAK 17(15Q26.1) WILD-TYPE   5 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      0   27
  AMP PEAK 17(15Q26.1) WILD-TYPE    5  321
                        clus
vv                       AMP PEAK 17(15Q26.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       AMP PEAK 17(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            321
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(16P11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(16P11.2) MUTATED   136  29
  AMP PEAK 18(16P11.2) WILD-TYPE 336  92
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           165                            428 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            29                             92 
$`AMP PEAK 18(16P11.2) MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 
       39.45        43.76        43.43        24.33        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       45.60        16.57        37.25        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 
       29.16        24.13        25.08        20.61        23.87        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 
       26.01        12.99        33.99        13.02        24.00        19.99 
TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 
       19.99        50.04        15.02        19.00        35.05        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3856 
       37.02        14.93        17.03        33.07         0.00         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       12.99        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G 
       26.01        27.02        34.03        42.02        15.02        12.00 
TCGA-AA-A01T TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       33.04        41.00        40.96        22.42        27.42         0.20 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
        0.95        33.01        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 
       29.56         5.23         1.61        12.69         3.29        14.30 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
      148.01        49.08         9.99        20.02         8.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       22.03        22.98        32.02        17.03         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 
       21.99        14.99        15.02        11.01        10.06        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 
       18.25         1.32        15.12        17.13        12.49         4.41 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 
        4.80        11.38        38.20        13.32        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       31.96         1.55        82.39        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 
       55.04        63.62        39.42        35.93        26.43        13.78 
TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2689 
       46.75        15.65        12.79        21.90        11.90        39.48 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        15.39        20.02        86.63        65.98 
TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 
       36.03        34.03         6.05        13.94        20.98         7.99 
TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 
       37.02        17.95        17.03        19.99        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
       46.03        15.95        36.03         9.07        12.00        31.00 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 
       38.96        38.04         0.72        10.19         6.97         9.37 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF 
       78.12        11.01         5.03         8.98         5.03        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 
       51.48         0.49        17.69        16.31        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        0.39        32.19         0.76 

$`AMP PEAK 18(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 
       43.76        42.90        42.28        13.94        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        36.53        14.53        32.91        31.63        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-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 
       34.03        29.00         0.99        14.01        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       47.05        47.01        11.01         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
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-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        10.06         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        18.05        31.00        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
       15.52        56.55         0.79         0.72         5.79        10.88 
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-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19         3.06         2.14         3.25         0.07 
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         1.91       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 
       12.26        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         1.48 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        3.68        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 
        1.51        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-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        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        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
       47.41        35.31       133.18        28.21         8.35        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       67.30        53.62        85.48        61.91        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       26.04        35.80        26.17        91.79        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 
       18.18        10.98        19.33        19.33         9.93        17.85 
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-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        70.03        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N 
       19.10        34.49        14.50        16.83        10.39        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 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-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        29.98        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
        1.02        48.03        32.02        28.04        14.04        17.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        3.98        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       37.02         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        41.00        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
        0.69        26.43         1.81         6.05        33.17         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       12.39         7.17        21.01        15.02        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         4.01         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 
       17.46        11.97         8.45         9.96        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                             0                              0 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                        20.980                         19.495 
[1] "0.0 - 148.0 (21.0)" "0.0 - 140.4 (19.5)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   124  47
  AMP PEAK 18(16P11.2) WILD-TYPE 322 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    124   47
  AMP PEAK 18(16P11.2) WILD-TYPE  322  115
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  COLON                           124                            322
  RECTUM                           47                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(16P11.2) MUTATED        20        1        4        39         3
  AMP PEAK 18(16P11.2) WILD-TYPE      84        0       32       134         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(16P11.2) MUTATED           0         7          9         31
  AMP PEAK 18(16P11.2) WILD-TYPE         3        19          9         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(16P11.2) MUTATED           21       23         8         1
  AMP PEAK 18(16P11.2) WILD-TYPE         33       40        18         1
D18V4, multiclass
            clus
vv           AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              1                              0
  STAGE II                              4                             32
  STAGE IIA                            39                            134
  STAGE IIB                             3                              7
  STAGE IIC                             0                              3
  STAGE III                             7                             19
  STAGE IIIA                            9                              9
  STAGE IIIB                           31                             52
  STAGE IIIC                           21                             33
  STAGE IV                             23                             40
  STAGE IVA                             8                             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 18(16P11.2) MUTATED     5  26 123  17
  AMP PEAK 18(16P11.2) WILD-TYPE  15  80 294  50
D18V5, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  T1                            5                             15
  T2                           26                             80
  T3                          123                            294
  T4                           17                             50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 18(16P11.2) MUTATED    73  55  43
  AMP PEAK 18(16P11.2) WILD-TYPE 272  95  72
D18V6, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  N0                           73                            272
  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"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   116  32
  AMP PEAK 18(16P11.2) WILD-TYPE 334  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    116   32
  AMP PEAK 18(16P11.2) WILD-TYPE  334   56
   clus
vv  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  0                          116                            334
  1                           32                             56
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED    81  91
  AMP PEAK 18(16P11.2) WILD-TYPE 206 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED     81   91
  AMP PEAK 18(16P11.2) WILD-TYPE  206  234
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  FEMALE                           81                            206
  MALE                             91                            234
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   129   9
  AMP PEAK 18(16P11.2) WILD-TYPE 317  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    129    9
  AMP PEAK 18(16P11.2) WILD-TYPE  317   19
     clus
vv    AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  NO                           129                            317
  YES                            9                             19
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                    115
  AMP PEAK 18(16P11.2) WILD-TYPE                  267
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                               7
  AMP PEAK 18(16P11.2) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                      47
  AMP PEAK 18(16P11.2) WILD-TYPE                    99
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                                0
  AMP PEAK 18(16P11.2) WILD-TYPE                             13
D18V10, multiclass
                                clus
vv                               AMP PEAK 18(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                    115
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 18(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      267
  COLON MUCINOUS ADENOCARCINOMA                              53
  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 18(16P11.2) MUTATED   125   0  14   7
  AMP PEAK 18(16P11.2) WILD-TYPE 317   5  23  22
D18V11, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  R0                          125                            317
  R1                            0                              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"
D18V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(16P11.2) MUTATED                                  1     3
  AMP PEAK 18(16P11.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(16P11.2) MUTATED                          19    83
  AMP PEAK 18(16P11.2) WILD-TYPE                        45   209
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK 18(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED     2  97
  AMP PEAK 18(16P11.2) WILD-TYPE   3 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED      2   97
  AMP PEAK 18(16P11.2) WILD-TYPE    3  251
                        clus
vv                       AMP PEAK 18(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       AMP PEAK 18(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            251
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(17Q12) MUTATED   131  22
  AMP PEAK 19(17Q12) WILD-TYPE 341  99
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         153                          440 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          22                           99 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 
       15.62        12.66         1.61        39.45        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 
       24.33        37.02        36.53        14.53        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-3496 TCGA-AA-3506 TCGA-AA-3517 
       20.28         1.02        37.05         1.02        58.03        38.99 
TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 
       36.03         0.00        29.00        12.99        24.00        23.01 
TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 
       15.02        36.00        85.05        35.05         1.02        17.03 
TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 
        0.99        24.03        27.02        18.05        12.99        34.03 
TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00L 
        2.01        50.99        13.05        27.02        27.02        38.04 
TCGA-AA-A00Z TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A02O TCGA-AA-A02W 
       21.99        32.02        12.00         1.02         0.92        41.00 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK 
       15.52         0.79        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         0.07 
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         2.96        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         1.32 
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         4.80        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 
       38.20       130.65         6.12        95.18         1.55        74.56 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       65.85        55.04        63.62        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX 
       26.43        46.75        15.65        17.85        29.46        32.98 
TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       30.28        17.23        86.63        65.98        11.84        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 
        7.07        36.03        46.03        34.03        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3898 
       13.94        19.99         0.99        19.99         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 
       32.02        36.03         1.02        17.03        15.95         9.07 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 
       31.00        64.01        51.98         0.69        26.43         6.05 
TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DG 
        9.37         8.98         4.01         5.03         5.29        51.48 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6813 
       17.00        18.28        16.31        11.97        32.19         0.69 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
       12.46        55.76        26.43 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
        4.80         9.53        43.76        46.65        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.25        34.65        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        22.52        24.13         8.38 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-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-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         1.02         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       37.05        19.00         5.03        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02        14.93         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03        32.05        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        29.98        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       33.01        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       16.08        34.06        26.01        25.02        24.00        19.07 
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         1.02        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-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        10.88         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.61         3.06         2.14         3.25         3.29        12.20 
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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
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-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-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-6677 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       10.06        12.03        45.40        12.26        56.09        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       20.42        17.75        43.27        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        16.24 
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-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
       28.21         8.35        82.39        23.51        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       44.68        85.48        61.91        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        74.79        79.69        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-T9-A92H TCGA-WS-AB45 
       42.77         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 
       10.39        36.03        32.02         8.02        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 
       37.02        32.98         0.99        19.04        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3909 
       17.03        13.02        35.01        14.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        36.03         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       61.97        41.00        38.04        38.56         1.45         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.81        10.19        33.17         6.97         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       28.57         0.39         0.66         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6572 
       18.28        47.08 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       19.99                        19.99 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D19V2, continuous
D19V3, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   114  46
  AMP PEAK 19(17Q12) WILD-TYPE 332 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    114   46
  AMP PEAK 19(17Q12) WILD-TYPE  332  116
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  COLON                         114                          332
  RECTUM                         46                          116
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(17Q12) MUTATED        22        0        7        42         1
  AMP PEAK 19(17Q12) WILD-TYPE      82        1       29       131         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(17Q12) MUTATED           1         6          4         21
  AMP PEAK 19(17Q12) WILD-TYPE         2        20         14         62
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(17Q12) MUTATED           18       25         9         1
  AMP PEAK 19(17Q12) WILD-TYPE         36       38        17         1
D19V4, multiclass
            clus
vv           AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  STAGE I                            22                           82
  STAGE IA                            0                            1
  STAGE II                            7                           29
  STAGE IIA                          42                          131
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           6                           20
  STAGE IIIA                          4                           14
  STAGE IIIB                         21                           62
  STAGE IIIC                         18                           36
  STAGE IV                           25                           38
  STAGE IVA                           9                           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 19(17Q12) MUTATED     8  21 115  16
  AMP PEAK 19(17Q12) WILD-TYPE  12  85 302  51
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                          8                           12
  T2                         21                           85
  T3                        115                          302
  T4                         16                           51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 19(17Q12) MUTATED    83  39  38
  AMP PEAK 19(17Q12) WILD-TYPE 262 111  77
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  N0                         83                          262
  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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   103  34
  AMP PEAK 19(17Q12) WILD-TYPE 347  54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    103   34
  AMP PEAK 19(17Q12) WILD-TYPE  347   54
   clus
vv  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  0                        103                          347
  1                         34                           54
[1] 2 2
[1] FALSE
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED    66  94
  AMP PEAK 19(17Q12) WILD-TYPE 221 231
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     66   94
  AMP PEAK 19(17Q12) WILD-TYPE  221  231
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  FEMALE                         66                          221
  MALE                           94                          231
[1] 2 2
[1] FALSE
D19V9, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   116   6
  AMP PEAK 19(17Q12) WILD-TYPE 330  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    116    6
  AMP PEAK 19(17Q12) WILD-TYPE  330   22
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NO                         116                          330
  YES                          6                           22
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                    101
  AMP PEAK 19(17Q12) WILD-TYPE                  281
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                              11
  AMP PEAK 19(17Q12) WILD-TYPE                            49
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                      44
  AMP PEAK 19(17Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                                2
  AMP PEAK 19(17Q12) WILD-TYPE                             11
D19V10, multiclass
                                clus
vv                               AMP PEAK 19(17Q12) MUTATED
  COLON ADENOCARCINOMA                                  101
  COLON MUCINOUS ADENOCARCINOMA                          11
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 19(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    281
  COLON MUCINOUS ADENOCARCINOMA                            49
  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 19(17Q12) MUTATED   110   2  16   6
  AMP PEAK 19(17Q12) WILD-TYPE 332   3  21  23
D19V11, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  R0                        110                          332
  R1                          2                            3
  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"
D19V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(17Q12) MUTATED                                  1     4
  AMP PEAK 19(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q12) MUTATED                          21    71
  AMP PEAK 19(17Q12) WILD-TYPE                        43   221
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                21
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 19(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  43
  WHITE                                                     221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED     3  90
  AMP PEAK 19(17Q12) WILD-TYPE   2 258
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      3   90
  AMP PEAK 19(17Q12) WILD-TYPE    2  258
                        clus
vv                       AMP PEAK 19(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         90
                        clus
vv                       AMP PEAK 19(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          258
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(17Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17Q24.1) MUTATED   122  17
  AMP PEAK 20(17Q24.1) WILD-TYPE 350 104
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           139                            454 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                            17                            104 
$`AMP PEAK 20(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2675 
       15.62         4.80        12.66         1.61        39.45        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 
       24.33        42.28        37.02        36.53        14.53        30.44 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 
       29.19        32.71        29.16        27.09        25.08        25.18 
TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
       24.69        20.28         1.02        37.05         1.02        58.03 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 
       24.00        23.01        15.02        36.00        85.05        35.05 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3867 
        1.02        17.03        10.06        36.03         0.99        24.03 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       12.99        24.00        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00Z 
       13.05        34.06        27.02        13.94        38.04        21.99 
TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 
       12.00         1.02        37.02        41.00        15.52         0.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 
       27.42        16.44        14.50        16.31        88.21        29.56 
TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       12.69         0.07       148.01         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03         2.96        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.26        19.59        55.92 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
        1.32        15.12         4.80        17.13        14.30         4.80 
TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 
      130.65         6.12        95.18        74.56        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 
       63.62        39.42        35.93        36.00        26.43        91.79 
TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL 
       46.75        15.65        17.85        29.46        32.98        30.28 
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-3612 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       19.99        19.99        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 
        9.07        31.00        51.98         0.69        26.43         6.05 
TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 
        8.98         4.01         5.03       129.27        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 
        2.40        18.28        16.31        11.97        32.19        12.46 
TCGA-G5-6235 
       55.76 

$`AMP PEAK 20(17Q24.1) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2679 
        9.53        43.76        46.65        43.76        42.90        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       22.09        22.06        22.52        24.13         8.38        24.16 
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-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-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        10.06         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       14.93         0.00         0.00        33.07         0.00        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-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-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        2.01        20.98        16.08        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        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         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
       35.01        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.72         5.79        22.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         1.61         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       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-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       15.02        14.04        11.01        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        45.40        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        1.48         3.68         4.41        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        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        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       67.30        53.62        44.68        85.48        61.91        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       16.80        42.77         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       70.03        24.13        43.04        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 
       65.98        36.03        32.02         8.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        34.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        13.94        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02        36.03         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       61.97        41.00        38.04        38.56         1.45         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.95         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
       32.61        20.55        19.96        20.91        17.00        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        47.08        26.43 

  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                         21.99                          19.99 
[1] "0.1 - 148.0 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.9"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED   105  38
  AMP PEAK 20(17Q24.1) WILD-TYPE 341 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED    105   38
  AMP PEAK 20(17Q24.1) WILD-TYPE  341  124
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON                           105                            341
  RECTUM                           38                            124
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(17Q24.1) MUTATED        21        0        4        42         2
  AMP PEAK 20(17Q24.1) WILD-TYPE      83        1       32       131         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(17Q24.1) MUTATED           1         6          3         22
  AMP PEAK 20(17Q24.1) WILD-TYPE         2        20         15         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(17Q24.1) MUTATED           12       19         8         1
  AMP PEAK 20(17Q24.1) WILD-TYPE         42       44        18         1
D20V4, multiclass
            clus
vv           AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  STAGE I                              21                             83
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            42                            131
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            3                             15
  STAGE IIIB                           22                             61
  STAGE IIIC                           12                             42
  STAGE IV                             19                             44
  STAGE IVA                             8                             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 20(17Q24.1) MUTATED     4  23 104  13
  AMP PEAK 20(17Q24.1) WILD-TYPE  16  83 313  54
D20V5, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  T1                            4                             16
  T2                           23                             83
  T3                          104                            313
  T4                           13                             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 20(17Q24.1) MUTATED    80  37  27
  AMP PEAK 20(17Q24.1) WILD-TYPE 265 113  88
D20V6, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  N0                           80                            265
  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"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED    96  27
  AMP PEAK 20(17Q24.1) WILD-TYPE 354  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED     96   27
  AMP PEAK 20(17Q24.1) WILD-TYPE  354   61
   clus
vv  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  0                           96                            354
  1                           27                             61
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED    70  74
  AMP PEAK 20(17Q24.1) WILD-TYPE 217 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED     70   74
  AMP PEAK 20(17Q24.1) WILD-TYPE  217  251
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  FEMALE                           70                            217
  MALE                             74                            251
[1] 2 2
[1] FALSE
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED   110   6
  AMP PEAK 20(17Q24.1) WILD-TYPE 336  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED    110    6
  AMP PEAK 20(17Q24.1) WILD-TYPE  336   22
     clus
vv    AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  NO                           110                            336
  YES                            6                             22
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                     94
  AMP PEAK 20(17Q24.1) WILD-TYPE                  288
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                              10
  AMP PEAK 20(17Q24.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                      38
  AMP PEAK 20(17Q24.1) WILD-TYPE                   108
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                                0
  AMP PEAK 20(17Q24.1) WILD-TYPE                             13
D20V10, multiclass
                                clus
vv                               AMP PEAK 20(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                     94
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      288
  COLON MUCINOUS ADENOCARCINOMA                              50
  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 20(17Q24.1) MUTATED   105   2  12   3
  AMP PEAK 20(17Q24.1) WILD-TYPE 337   3  25  26
D20V11, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  R0                          105                            337
  R1                            2                              3
  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"
D20V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(17Q24.1) MUTATED                                  0     2
  AMP PEAK 20(17Q24.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17Q24.1) MUTATED                          19    71
  AMP PEAK 20(17Q24.1) WILD-TYPE                        45   221
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      71
                                  clus
vv                                 AMP PEAK 20(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED     3  86
  AMP PEAK 20(17Q24.1) WILD-TYPE   2 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED      3   86
  AMP PEAK 20(17Q24.1) WILD-TYPE    2  262
                        clus
vv                       AMP PEAK 20(17Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 20(17Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            262
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.2) MUTATED    86  20
  AMP PEAK 21(19P13.2) WILD-TYPE 386 101
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           106                            487 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            20                            101 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 
       15.62        12.66        43.76        43.43        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       16.57        36.53        14.53        31.63        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 
       21.76        23.87        56.25         9.07         6.05         2.01 
TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 
       37.05        35.05         0.99        31.07        50.99        13.05 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O 
       27.02        13.94        42.02        32.02        51.98         0.92 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-A8YK 
        5.79        22.42        16.44         0.46        16.31        18.84 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       88.21        29.56        11.74         3.06        14.30        85.45 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
        9.99         1.91        25.02        13.02        29.06        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02         2.96        29.03        21.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 
       13.02        11.08        19.59        56.09        15.12        11.38 
TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       49.91        35.97        74.56        63.62        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2690 
       26.43        74.79        17.85        29.46        21.90        17.23 
TCGA-AF-3913 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3592 
       10.39        86.63        65.98        36.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3896 
        6.05        19.99        13.94         0.99        17.95         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N 
       28.04        36.03         1.02        46.03        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 
        1.94        38.04        21.01        11.01         8.98        27.95 
TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6512 
        4.01        57.24        24.13         0.49        20.55        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6863 
       16.31        11.51        11.97         0.76 

$`AMP PEAK 21(19P13.2) WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
        4.80         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
       42.90        24.33        42.28        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.25        37.02        34.65        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04        10.06        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 
       34.03         2.01        21.99        16.08        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07         7.96        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        26.01        37.02        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 
        0.72        27.42        10.88         0.20         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.61        12.69         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        49.08        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02        37.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 
       27.02        22.03        22.98        30.08        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       17.03        12.00        16.04        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        45.40        12.26        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        43.27        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         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         4.80         1.51        12.00        10.26       119.70 
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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       85.48        35.93        61.91        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        46.75        79.69        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        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        24.13        39.48        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        34.49        37.74        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        10.39        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        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-3887 
       32.98         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       19.99        14.04        17.03         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        41.00        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.17        15.02         5.03        13.97        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48        32.61         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.41         8.61 
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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                          0.46                           0.00 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         88.21                         148.01 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         20.78                          19.99 
[1] "0.5 - 88.2 (20.8)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    75  36
  AMP PEAK 21(19P13.2) WILD-TYPE 371 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     75   36
  AMP PEAK 21(19P13.2) WILD-TYPE  371  126
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  COLON                            75                            371
  RECTUM                           36                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(19P13.2) MUTATED        14        0        6        28         2
  AMP PEAK 21(19P13.2) WILD-TYPE      90        1       30       145         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(19P13.2) MUTATED           1         6          2         21
  AMP PEAK 21(19P13.2) WILD-TYPE         2        20         16         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(19P13.2) MUTATED           11       12         6         0
  AMP PEAK 21(19P13.2) WILD-TYPE         43       51        20         2
D21V4, multiclass
            clus
vv           AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  STAGE I                              14                             90
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            28                            145
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            2                             16
  STAGE IIIB                           21                             62
  STAGE IIIC                           11                             43
  STAGE IV                             12                             51
  STAGE IVA                             6                             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
  AMP PEAK 21(19P13.2) MUTATED     2  15  81  13
  AMP PEAK 21(19P13.2) WILD-TYPE  18  91 336  54
D21V5, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  T1                            2                             18
  T2                           15                             91
  T3                           81                            336
  T4                           13                             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 21(19P13.2) MUTATED    55  36  20
  AMP PEAK 21(19P13.2) WILD-TYPE 290 114  95
D21V6, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  N0                           55                            290
  N1                           36                            114
  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"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    74  18
  AMP PEAK 21(19P13.2) WILD-TYPE 376  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     74   18
  AMP PEAK 21(19P13.2) WILD-TYPE  376   70
   clus
vv  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  0                           74                            376
  1                           18                             70
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    47  64
  AMP PEAK 21(19P13.2) WILD-TYPE 240 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     47   64
  AMP PEAK 21(19P13.2) WILD-TYPE  240  261
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  FEMALE                           47                            240
  MALE                             64                            261
[1] 2 2
[1] FALSE
D21V9, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    79   8
  AMP PEAK 21(19P13.2) WILD-TYPE 367  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     79    8
  AMP PEAK 21(19P13.2) WILD-TYPE  367   20
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  NO                            79                            367
  YES                            8                             20
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                     67
  AMP PEAK 21(19P13.2) WILD-TYPE                  315
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                               8
  AMP PEAK 21(19P13.2) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                      36
  AMP PEAK 21(19P13.2) WILD-TYPE                   110
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                                0
  AMP PEAK 21(19P13.2) WILD-TYPE                             13
D21V10, multiclass
                                clus
vv                               AMP PEAK 21(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                     67
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 21(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      315
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     110
  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 21(19P13.2) MUTATED    80   3   6   7
  AMP PEAK 21(19P13.2) WILD-TYPE 362   2  31  22
D21V11, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  R0                           80                            362
  R1                            3                              2
  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"
D21V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(19P13.2) MUTATED                                  0     2
  AMP PEAK 21(19P13.2) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19P13.2) MUTATED                          17    57
  AMP PEAK 21(19P13.2) WILD-TYPE                        47   235
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 21(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED     0  72
  AMP PEAK 21(19P13.2) WILD-TYPE   5 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED      0   72
  AMP PEAK 21(19P13.2) WILD-TYPE    5  276
                        clus
vv                       AMP PEAK 21(19P13.2) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       AMP PEAK 21(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(19Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(19Q12) MUTATED   107  23
  AMP PEAK 22(19Q12) WILD-TYPE 365  98
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         130                          463 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          23                           98 
$`AMP PEAK 22(19Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 
       15.62        12.66        39.45        43.76        43.43        45.60 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       16.57        37.02        34.65        36.53        14.53        31.63 
TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 
       29.16        25.08        25.18        21.76        23.87        61.84 
TCGA-A6-A56B TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 
       56.25        35.01        58.03        12.99        13.02        37.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 
       35.05         0.99        37.02        33.07        36.03        12.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z 
       50.99        13.05        18.05        27.02        42.02        21.99 
TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 
       12.00        51.98         2.96        39.98         0.92        15.52 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-A69D 
        5.79        22.42         0.20        16.44        14.50        17.85 
TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 
       18.84        88.21        29.56        11.74         3.06        14.30 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
       85.45         9.99         1.91        37.02        25.02        13.02 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       32.02         5.03        15.02        15.02         2.96        29.03 
TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 
       21.99        11.08        19.59        15.12         4.80        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 
        4.80        12.00        11.38       119.70        35.97         8.61 
TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       47.41        82.39        74.56        63.62        39.42        26.43 
TCGA-G4-6627 TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3913 
       74.79        17.85        29.46        21.90        39.48        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       86.63        65.98        36.03        46.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 
        6.05        19.99        20.98         0.99        19.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       36.03         1.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 
       31.00         1.94        38.04        10.19         6.05         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 
       12.39        21.01        11.01         8.98        27.95         4.01 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 
      129.27        24.13         0.49        20.55        17.69        16.31 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 
       11.51        13.64        11.97         0.76 

$`AMP PEAK 22(19Q12) WILD-TYPE`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
       24.33        42.28        44.91        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       37.25        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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        24.16        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       20.12        19.66        20.28        16.24        24.92         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        19.04        10.06        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       17.03        10.06         0.00         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        38.04         4.01 
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         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.06         2.01         5.03        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72        27.42        10.88         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-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 
       12.20        12.76        10.06        17.56       148.01        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        49.08        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 
       23.05        20.02        26.04         8.02        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 
       22.03        22.98        30.08        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       12.00        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85        17.13        12.49        16.14        15.58         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        12.43        14.30         9.04         9.44 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        1.51        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-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        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-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       13.25         0.53        35.31       133.18        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       85.48        35.93        61.91        36.00        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        79.69 
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-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        42.77        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       30.28        11.90        70.03        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        34.49        37.74        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        20.02        10.39        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
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-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       13.94        19.99         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        14.04        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81        33.17         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       78.12         7.17        15.02         5.03        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 
       41.36        57.24        51.48        32.61         2.40        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-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
        8.61        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         0.2                          0.0 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                      129.27                       148.01 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                       20.27                        19.99 
[1] "0.2 - 129.3 (20.3)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D22V2, continuous
D22V3, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    95  44
  AMP PEAK 22(19Q12) WILD-TYPE 351 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     95   44
  AMP PEAK 22(19Q12) WILD-TYPE  351  118
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  COLON                          95                          351
  RECTUM                         44                          118
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(19Q12) MUTATED        22        0        5        36         1
  AMP PEAK 22(19Q12) WILD-TYPE      82        1       31       137         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(19Q12) MUTATED           1         5          3         22
  AMP PEAK 22(19Q12) WILD-TYPE         2        21         15         61
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(19Q12) MUTATED           13       22         6         0
  AMP PEAK 22(19Q12) WILD-TYPE         41       41        20         2
D22V4, multiclass
            clus
vv           AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  STAGE I                            22                           82
  STAGE IA                            0                            1
  STAGE II                            5                           31
  STAGE IIA                          36                          137
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          3                           15
  STAGE IIIB                         22                           61
  STAGE IIIC                         13                           41
  STAGE IV                           22                           41
  STAGE IVA                           6                           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
  AMP PEAK 22(19Q12) MUTATED     3  22  98  16
  AMP PEAK 22(19Q12) WILD-TYPE  17  84 319  51
D22V5, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  T1                          3                           17
  T2                         22                           84
  T3                         98                          319
  T4                         16                           51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 22(19Q12) MUTATED    69  43  27
  AMP PEAK 22(19Q12) WILD-TYPE 276 107  88
D22V6, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  N0                         69                          276
  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"
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    90  28
  AMP PEAK 22(19Q12) WILD-TYPE 360  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     90   28
  AMP PEAK 22(19Q12) WILD-TYPE  360   60
   clus
vv  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  0                         90                          360
  1                         28                           60
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    59  80
  AMP PEAK 22(19Q12) WILD-TYPE 228 245
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     59   80
  AMP PEAK 22(19Q12) WILD-TYPE  228  245
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  FEMALE                         59                          228
  MALE                           80                          245
[1] 2 2
[1] FALSE
D22V9, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    98   8
  AMP PEAK 22(19Q12) WILD-TYPE 348  20
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     98    8
  AMP PEAK 22(19Q12) WILD-TYPE  348   20
     clus
vv    AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  NO                          98                          348
  YES                          8                           20
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                     85
  AMP PEAK 22(19Q12) WILD-TYPE                  297
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                              10
  AMP PEAK 22(19Q12) WILD-TYPE                            50
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                      44
  AMP PEAK 22(19Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                                0
  AMP PEAK 22(19Q12) WILD-TYPE                             13
D22V10, multiclass
                                clus
vv                               AMP PEAK 22(19Q12) MUTATED
  COLON ADENOCARCINOMA                                   85
  COLON MUCINOUS ADENOCARCINOMA                          10
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          0
                                clus
vv                               AMP PEAK 22(19Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    297
  COLON MUCINOUS ADENOCARCINOMA                            50
  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 22(19Q12) MUTATED    98   2  11   7
  AMP PEAK 22(19Q12) WILD-TYPE 344   3  26  22
D22V11, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  R0                         98                          344
  R1                          2                            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"
D22V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(19Q12) MUTATED                                  0     2
  AMP PEAK 22(19Q12) WILD-TYPE                                1    10
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(19Q12) MUTATED                          19    70
  AMP PEAK 22(19Q12) WILD-TYPE                        45   222
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                19
  WHITE                                                    70
                                  clus
vv                                 AMP PEAK 22(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                  45
  WHITE                                                     222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED     2  84
  AMP PEAK 22(19Q12) WILD-TYPE   3 264
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED      2   84
  AMP PEAK 22(19Q12) WILD-TYPE    3  264
                        clus
vv                       AMP PEAK 22(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       AMP PEAK 22(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          264
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(20P12.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(20P12.1) MUTATED   216  53
  AMP PEAK 23(20P12.1) WILD-TYPE 256  68
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           269                            324 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                            53                             68 
$`AMP PEAK 23(20P12.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       15.62         4.80        39.45        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 
       44.91        35.11        45.60        13.94        16.57        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6137 
       34.65        36.53        32.45        32.91        30.44        27.09 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       25.08        24.16        24.69        20.28        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 
        5.03         7.04         1.02        58.03         6.97         1.02 
TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 
       24.03         0.00        19.07        29.00        29.00        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3662 
       21.01        13.02        23.01        20.98        19.99         6.05 
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-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 
       19.00        36.00         5.03        10.06         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       14.93         0.00        17.03        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 
       31.07        17.03        18.05        12.99        24.00        34.03 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       21.99        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L 
       27.02        19.07         7.96        13.94        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D 
        4.01        17.03        14.99        21.99        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E 
       12.00        31.00        33.04        26.01        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 
        2.01         5.03         0.92        41.00        39.98         0.07 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        0.79         0.72         5.79        22.42        27.42        16.44 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       16.31         0.95        17.26        17.85        19.33        18.84 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-6598 TCGA-AZ-6600 
        1.41         5.13       106.75        65.00        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       29.56         3.19        12.69         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-4744 
        0.07        14.30        17.56        85.45        49.08        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         2.96        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        12.26 
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         3.68         4.41 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04        11.64         4.80        10.26       119.70        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
        7.50        44.32       139.17         6.12        14.04        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
      117.07        95.18         8.61        35.74         6.18         1.55 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6310 
       47.41       133.18        28.21        82.39        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 
       39.42        35.93        36.00        26.04        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       46.75        74.79        18.18        15.65        12.79        17.85 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 
       42.77        29.46        32.98        24.13        17.23        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        16.83        20.02        10.39 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        8.02        36.03         1.02        46.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       50.04        12.03         0.99        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 
       20.98        29.98        37.02         0.99        36.95        17.03 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       14.01        48.03        19.99        14.04         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       51.98        41.00        38.04        38.56         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       12.39        21.01        11.01        15.02         5.03        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EI-6506 
       15.02        27.95         5.95       126.44       129.27        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6885 TCGA-EI-7002 
       20.91        17.00        18.28        16.31        13.64        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
        9.96        49.51         0.39        32.19         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        18.28        55.76        47.08 

$`AMP PEAK 23(20P12.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
       12.66         1.61         9.53        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5660 
       42.28        37.05        37.25        14.53        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13         8.38        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
       56.25         3.02        37.05         1.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        34.03        26.01        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       33.99        24.00        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       61.02        78.08         6.97        54.02         0.92        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       36.95         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        27.02        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        20.98         2.01 
TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       16.08        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        1.02        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R 
        1.02        35.01        37.02        39.06        39.98        22.03 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 
       18.05        40.96        21.37        15.52        56.55        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
        0.20         0.46         0.92        14.50        27.09        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       21.44        17.82       109.28        75.95        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       32.94        22.36        62.79        88.21         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        5.23        11.74         1.61         3.25        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       10.06       148.01        70.16        15.62        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14        82.95         1.91       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       26.04         8.02        27.02        22.03        30.08        32.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        29.03        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       15.02        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
        1.48        12.43        14.30         9.44         1.51        12.00 
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-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A 
       13.32       140.38       131.51       135.65         7.76        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 
       81.37       119.93        60.79        98.24        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       13.25         0.53        35.31         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       67.30        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U 
       26.43        22.09        35.80        26.17        79.69        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       19.33        19.33         9.93        16.80         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 
       21.90        30.28        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        15.39        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-A014 TCGA-AG-A01J 
        3.98        46.03        20.98        13.94        15.95         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       12.00        31.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 TCGA-CI-6624 
        1.94        38.96        61.97         1.45        33.17         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       78.12         7.17         8.98        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.03         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6512 
       32.61         0.49         2.40        19.96        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
        8.45        31.30        28.57         0.69        12.46        26.43 

  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                             0                              0 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                        139.17                         148.01 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                        18.050                         22.075 
[1] "0.0 - 139.2 (18.1)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   194  81
  AMP PEAK 23(20P12.1) WILD-TYPE 252  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    194   81
  AMP PEAK 23(20P12.1) WILD-TYPE  252   81
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  COLON                           194                            252
  RECTUM                           81                             81
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20P12.1) MUTATED        50        1       10        69         4
  AMP PEAK 23(20P12.1) WILD-TYPE      54        0       26       104         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20P12.1) MUTATED           1        10         11         33
  AMP PEAK 23(20P12.1) WILD-TYPE         2        16          7         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20P12.1) MUTATED           24       42        13         1
  AMP PEAK 23(20P12.1) WILD-TYPE         30       21        13         1
D23V4, multiclass
            clus
vv           AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  STAGE I                              50                             54
  STAGE IA                              1                              0
  STAGE II                             10                             26
  STAGE IIA                            69                            104
  STAGE IIB                             4                              6
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                           11                              7
  STAGE IIIB                           33                             50
  STAGE IIIC                           24                             30
  STAGE IV                             42                             21
  STAGE IVA                            13                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 23(20P12.1) MUTATED     9  52 185  30
  AMP PEAK 23(20P12.1) WILD-TYPE  11  54 232  37
D23V5, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  T1                            9                             11
  T2                           52                             54
  T3                          185                            232
  T4                           30                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 23(20P12.1) MUTATED   143  75  58
  AMP PEAK 23(20P12.1) WILD-TYPE 202  75  57
D23V6, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  N0                          143                            202
  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"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   186  54
  AMP PEAK 23(20P12.1) WILD-TYPE 264  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    186   54
  AMP PEAK 23(20P12.1) WILD-TYPE  264   34
   clus
vv  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  0                          186                            264
  1                           54                             34
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   117 161
  AMP PEAK 23(20P12.1) WILD-TYPE 170 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    117  161
  AMP PEAK 23(20P12.1) WILD-TYPE  170  164
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  FEMALE                          117                            170
  MALE                            161                            164
[1] 2 2
[1] FALSE
D23V9, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   198  18
  AMP PEAK 23(20P12.1) WILD-TYPE 248  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    198   18
  AMP PEAK 23(20P12.1) WILD-TYPE  248   10
     clus
vv    AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  NO                           198                            248
  YES                           18                             10
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                    175
  AMP PEAK 23(20P12.1) WILD-TYPE                  207
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                              18
  AMP PEAK 23(20P12.1) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                      76
  AMP PEAK 23(20P12.1) WILD-TYPE                    70
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                                3
  AMP PEAK 23(20P12.1) WILD-TYPE                             10
D23V10, multiclass
                                clus
vv                               AMP PEAK 23(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    175
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                    76
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK 23(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      207
  COLON MUCINOUS ADENOCARCINOMA                              42
  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 23(20P12.1) MUTATED   198   3  23  10
  AMP PEAK 23(20P12.1) WILD-TYPE 244   2  14  19
D23V11, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  R0                          198                            244
  R1                            3                              2
  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"
D23V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(20P12.1) MUTATED                                  1     6
  AMP PEAK 23(20P12.1) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20P12.1) MUTATED                          27   132
  AMP PEAK 23(20P12.1) WILD-TYPE                        37   160
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK 23(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED     2 154
  AMP PEAK 23(20P12.1) WILD-TYPE   3 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED      2  154
  AMP PEAK 23(20P12.1) WILD-TYPE    3  194
                        clus
vv                       AMP PEAK 23(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          154
                        clus
vv                       AMP PEAK 23(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            194
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(20P11.21) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(20P11.21) MUTATED   282  68
  AMP PEAK 24(20P11.21) WILD-TYPE 190  53
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            350                             243 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                             68                              53 
$`AMP PEAK 24(20P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       32.91        30.44        29.19        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6782 
       24.13        25.08        25.18        24.16        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3496 
       61.84         9.63         5.03         7.04         1.02         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3530 
       58.03         6.97         1.02        38.99         0.00        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       29.00        29.00        12.99        14.01        21.01        13.02 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       23.01        20.98        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.05        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
       36.00         5.03        85.05        10.06         0.99        25.02 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        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-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L 
       27.02        19.07         7.96        13.94        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
        4.01        17.03        14.99        21.99         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       10.98        12.00        31.00        33.04        26.01        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-6548 TCGA-AD-6890 TCGA-AD-6895 
       39.98        40.96         0.07        21.37         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        5.79        22.42        27.42         0.20        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       16.31         0.95        17.26        17.85        19.33        18.84 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13       106.75        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.29         0.07        12.20        14.30        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
       85.45        49.08         9.99        20.02        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        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         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        13.02        15.02        14.04        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        17.75        18.25         1.32        43.27 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 
       12.49         1.48         3.68         4.41         9.04        11.64 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 
        4.80        10.26       119.70        24.43       130.65        12.59 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        14.04       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        95.18         8.61        31.96        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 
        6.18         1.55        33.67        13.25        47.41       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 
       28.21         8.35        82.39        23.51        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 
       55.04        63.62        39.42        35.93        61.91        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       13.78        91.79        46.75        74.79        18.18        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 
       21.90        11.90        24.13        39.48        17.23        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        10.39        16.83        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 
       11.84        36.03         8.02         7.07        36.03        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
       34.03        34.03        34.03        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
       19.99        13.94        19.99        20.98         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       37.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       64.01        51.98        41.00        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.72        26.43         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG 
        5.95         4.01       126.44        41.36       129.27        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        0.49        20.55        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.31        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 24(20P11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       12.66         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-2685 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       37.25        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       32.71         8.38        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-3516 TCGA-AA-3518 TCGA-AA-3519 
       37.05        35.01        63.98        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       26.01         0.99        33.99        24.00        17.95        29.95 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       19.99        13.94        61.02         6.97        54.02         0.92 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       47.01        11.01         5.98        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 
       35.05         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 
        0.00        36.03        32.05        31.07        53.00        24.03 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        2.01        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       32.02        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6888 
       35.01        37.02        39.06        22.03        18.05        15.52 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
       56.55        10.88         0.46         0.92        27.09        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       21.44        17.82       109.28        75.95        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       32.94        22.36        88.21         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 
       11.74         3.25        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         1.91       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 
        1.51        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        16.24         0.53        35.31        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       67.30        53.62        85.48        36.00        26.43        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        79.69        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 
        9.93        16.80        31.30        30.28        70.03        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3575 
       13.55        34.49        14.50        15.39        65.98        12.00 
TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3600 
       32.02        20.05        24.00         1.02         2.01         6.05 
TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3892 
        0.99         0.99        32.98        19.04        17.95        13.02 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       35.01        28.04         3.98        46.03        20.98        13.94 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        1.02        31.00        70.03        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-6158 
       38.96        61.97         1.45        33.17         4.73        10.98 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       19.99         5.03         5.29        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        2.40        19.96        15.85        16.34        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
       17.46         8.45        31.30 

  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                         139.17                          148.01 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                         18.265                          22.360 
[1] "0.0 - 139.2 (18.3)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   250 110
  AMP PEAK 24(20P11.21) WILD-TYPE 196  52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    250  110
  AMP PEAK 24(20P11.21) WILD-TYPE  196   52
        clus
vv       AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  COLON                            250                             196
  RECTUM                           110                              52
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 24(20P11.21) MUTATED        64        1       16        97         5
  AMP PEAK 24(20P11.21) WILD-TYPE      40        0       20        76         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(20P11.21) MUTATED           2        11         15         45
  AMP PEAK 24(20P11.21) WILD-TYPE         1        15          3         38
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20P11.21) MUTATED           30       48        17         1
  AMP PEAK 24(20P11.21) WILD-TYPE         24       15         9         1
D24V4, multiclass
            clus
vv           AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  STAGE I                               64                              40
  STAGE IA                               1                               0
  STAGE II                              16                              20
  STAGE IIA                             97                              76
  STAGE IIB                              5                               5
  STAGE IIC                              2                               1
  STAGE III                             11                              15
  STAGE IIIA                            15                               3
  STAGE IIIB                            45                              38
  STAGE IIIC                            30                              24
  STAGE IV                              48                              15
  STAGE IVA                             17                               9
  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(20P11.21) MUTATED    13  67 243  37
  AMP PEAK 24(20P11.21) WILD-TYPE   7  39 174  30
D24V5, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  T1                            13                               7
  T2                            67                              39
  T3                           243                             174
  T4                            37                              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 24(20P11.21) MUTATED   197  95  68
  AMP PEAK 24(20P11.21) WILD-TYPE 148  55  47
D24V6, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  N0                           197                             148
  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"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   250  65
  AMP PEAK 24(20P11.21) WILD-TYPE 200  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    250   65
  AMP PEAK 24(20P11.21) WILD-TYPE  200   23
   clus
vv  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  0                           250                             200
  1                            65                              23
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   158 204
  AMP PEAK 24(20P11.21) WILD-TYPE 129 121
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    158  204
  AMP PEAK 24(20P11.21) WILD-TYPE  129  121
        clus
vv       AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  FEMALE                           158                             129
  MALE                             204                             121
[1] 2 2
[1] FALSE
D24V9, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   257  20
  AMP PEAK 24(20P11.21) WILD-TYPE 189   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    257   20
  AMP PEAK 24(20P11.21) WILD-TYPE  189    8
     clus
vv    AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  NO                            257                             189
  YES                            20                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                    227
  AMP PEAK 24(20P11.21) WILD-TYPE                  155
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                              22
  AMP PEAK 24(20P11.21) WILD-TYPE                            38
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                     105
  AMP PEAK 24(20P11.21) WILD-TYPE                    41
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                                4
  AMP PEAK 24(20P11.21) WILD-TYPE                              9
D24V10, multiclass
                                clus
vv                               AMP PEAK 24(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                     227
  COLON MUCINOUS ADENOCARCINOMA                             22
  RECTAL ADENOCARCINOMA                                    105
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               AMP PEAK 24(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       155
  COLON MUCINOUS ADENOCARCINOMA                               38
  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 24(20P11.21) MUTATED   260   3  25  14
  AMP PEAK 24(20P11.21) WILD-TYPE 182   2  12  15
D24V11, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  R0                           260                             182
  R1                             3                               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"
D24V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(20P11.21) MUTATED                                  1     7
  AMP PEAK 24(20P11.21) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(20P11.21) MUTATED                          36   179
  AMP PEAK 24(20P11.21) WILD-TYPE                        28   113
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      179
                                  clus
vv                                 AMP PEAK 24(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     28
  WHITE                                                        113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED     4 207
  AMP PEAK 24(20P11.21) WILD-TYPE   1 141
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED      4  207
  AMP PEAK 24(20P11.21) WILD-TYPE    1  141
                        clus
vv                       AMP PEAK 24(20P11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           207
                        clus
vv                       AMP PEAK 24(20P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             141
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(20Q11.21) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(20Q11.21) MUTATED   363  88
  AMP PEAK 25(20Q11.21) WILD-TYPE 109  33
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            451                             142 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                             88                              33 
$`AMP PEAK 25(20Q11.21) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.45        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.16        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-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05         1.02        58.03         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
        9.07        36.03        19.07         0.00        19.07        34.03 
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-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       19.00        36.00         5.03        85.05        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        0.99        25.02        38.99        36.95        37.02        14.93 
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-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        19.07         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        38.04         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       12.00        31.00        31.00         1.02        33.04        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-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        41.00        39.98        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       15.52         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.20        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       33.01        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         2.14         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
       14.30        17.56       148.01        85.45        49.08         9.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        1.91        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         2.96        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        12.26        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         1.32        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         1.48         3.68         4.41 
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         4.80        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        31.96        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        41.42        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       23.51        65.85        44.68        55.04        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       35.93        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       91.79        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        17.85        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
        8.42        21.90        30.28        11.90        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03         8.02         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-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       46.03        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        19.99         5.95         4.01         5.03       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-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK 25(20Q11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       12.66         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       31.63        33.53        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-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       63.98        13.02         1.02        24.03        37.05         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
        0.99        17.95        29.95        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 
        0.92        11.01        26.99        19.04        19.04         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-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 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-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
        0.99        34.98        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 
       39.06        22.03        18.05        56.55        10.88         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       27.09        21.44        17.82        75.95        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 
       32.94        88.21         6.77       100.01        11.74         3.25 
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         1.51        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-F4-6805 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       34.42        35.31        74.56        67.30        53.62        85.48 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       22.09        35.80        26.17        79.69        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-CI-6620 TCGA-DT-5265 
        3.98        20.98        49.97        61.97        33.17         5.29 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       19.96         8.61        17.46         8.45 

  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                         19.330                          22.075 
[1] "0.0 - 148.0 (19.3)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   319 144
  AMP PEAK 25(20Q11.21) WILD-TYPE 127  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    319  144
  AMP PEAK 25(20Q11.21) WILD-TYPE  127   18
        clus
vv       AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  COLON                            319                             127
  RECTUM                           144                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 25(20Q11.21) MUTATED        79        1       21       119         5
  AMP PEAK 25(20Q11.21) WILD-TYPE      25        0       15        54         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(20Q11.21) MUTATED           3        20         17         67
  AMP PEAK 25(20Q11.21) WILD-TYPE         0         6          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(20Q11.21) MUTATED           44       56        22         1
  AMP PEAK 25(20Q11.21) WILD-TYPE         10        7         4         1
D25V4, multiclass
            clus
vv           AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  STAGE I                               79                              25
  STAGE IA                               1                               0
  STAGE II                              21                              15
  STAGE IIA                            119                              54
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             20                               6
  STAGE IIIA                            17                               1
  STAGE IIIB                            67                              16
  STAGE IIIC                            44                              10
  STAGE IV                              56                               7
  STAGE IVA                             22                               4
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(20Q11.21) MUTATED    14  85 320  45
  AMP PEAK 25(20Q11.21) WILD-TYPE   6  21  97  22
D25V5, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  T1                            14                               6
  T2                            85                              21
  T3                           320                              97
  T4                            45                              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 25(20Q11.21) MUTATED   243 128  93
  AMP PEAK 25(20Q11.21) WILD-TYPE 102  22  22
D25V6, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  N0                           243                             102
  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"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   333  77
  AMP PEAK 25(20Q11.21) WILD-TYPE 117  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    333   77
  AMP PEAK 25(20Q11.21) WILD-TYPE  117   11
   clus
vv  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  0                           333                             117
  1                            77                              11
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   212 254
  AMP PEAK 25(20Q11.21) WILD-TYPE  75  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    212  254
  AMP PEAK 25(20Q11.21) WILD-TYPE   75   71
        clus
vv       AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  FEMALE                           212                              75
  MALE                             254                              71
[1] 2 2
[1] FALSE
D25V9, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   331  24
  AMP PEAK 25(20Q11.21) WILD-TYPE 115   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    331   24
  AMP PEAK 25(20Q11.21) WILD-TYPE  115    4
     clus
vv    AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  NO                            331                             115
  YES                            24                               4
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                    291
  AMP PEAK 25(20Q11.21) WILD-TYPE                   91
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                              25
  AMP PEAK 25(20Q11.21) WILD-TYPE                            35
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                     135
  AMP PEAK 25(20Q11.21) WILD-TYPE                    11
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                                7
  AMP PEAK 25(20Q11.21) WILD-TYPE                              6
D25V10, multiclass
                                clus
vv                               AMP PEAK 25(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                     291
  COLON MUCINOUS ADENOCARCINOMA                             25
  RECTAL ADENOCARCINOMA                                    135
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 25(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                        91
  COLON MUCINOUS ADENOCARCINOMA                               35
  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 25(20Q11.21) MUTATED   335   4  32  17
  AMP PEAK 25(20Q11.21) WILD-TYPE 107   1   5  12
D25V11, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  R0                           335                             107
  R1                             4                               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"
D25V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(20Q11.21) MUTATED                                  1     7
  AMP PEAK 25(20Q11.21) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(20Q11.21) MUTATED                          47   228
  AMP PEAK 25(20Q11.21) WILD-TYPE                        17    64
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      228
                                  clus
vv                                 AMP PEAK 25(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                         64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED     4 265
  AMP PEAK 25(20Q11.21) WILD-TYPE   1  83
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED      4  265
  AMP PEAK 25(20Q11.21) WILD-TYPE    1   83
                        clus
vv                       AMP PEAK 25(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           265
                        clus
vv                       AMP PEAK 25(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              83
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(20Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(20Q12) MUTATED   365  88
  AMP PEAK 26(20Q12) WILD-TYPE 107  33
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         453                          140 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                          88                           33 
$`AMP PEAK 26(20Q12) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.45        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.16        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-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05         1.02        58.03         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
        9.07        36.03        19.07         0.00        19.07        34.03 
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-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.05        47.01        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        85.05        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
       31.07        17.03        24.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       19.07         7.96        13.94        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99         1.02        15.02        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-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        40.96         0.07        21.37        15.52         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         5.79        22.42        27.42         0.20        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
        0.46        14.50        16.31         0.95        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33        18.84       109.28         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13       106.75        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       17.56       148.01        85.45        49.08         9.99         1.91 
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         2.96        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 
       12.26        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         1.32        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         1.48         3.68         4.41        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         4.80        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
        6.12        14.04        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        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        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       39.42        35.93        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       13.78        91.79        46.75        74.79        18.18        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 
       32.98         8.42        21.90        30.28        11.90        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       39.48        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        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-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        46.03        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`AMP PEAK 26(20Q12) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       12.66         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       31.63        33.53        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-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       63.98        13.02         1.02        24.03        37.05         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
        0.99        17.95        29.95        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        0.92        11.01         5.98        26.99        19.04        19.04 
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-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        27.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q 
       18.05         0.99        34.98        10.98        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
       35.01        35.01        39.06        22.03        18.05        56.55 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
       10.88         0.92        27.09        21.44        17.82        75.95 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       58.39        32.94        88.21         6.77       100.01        11.74 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        3.25        12.76        10.06        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 
       21.14        82.95       124.27        23.05        26.04        27.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 
       15.02        12.00        12.95        13.05        12.03        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 
       16.14        15.58         9.44         1.51        12.00       140.38 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 
      135.65         7.76        81.37        60.79        98.24        11.11 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       47.87        35.31        67.30        53.62        85.48        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       35.80        26.17        79.69        10.98        19.33         9.93 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
       31.30        70.03        13.55        34.49        12.00        32.02 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 
        2.01         6.05        32.98        19.04        13.02         3.98 
TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
       20.98        49.97        61.97         5.29        19.96         8.61 
TCGA-EI-6917 TCGA-EI-7004 
       17.46         8.45 

  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                      19.990                       21.735 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (21.7)"
[1] "hr=" "1.1"
D26V2, continuous
D26V3, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   320 145
  AMP PEAK 26(20Q12) WILD-TYPE 126  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    320  145
  AMP PEAK 26(20Q12) WILD-TYPE  126   17
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  COLON                         320                          126
  RECTUM                        145                           17
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 26(20Q12) MUTATED        79        1       21       120         5
  AMP PEAK 26(20Q12) WILD-TYPE      25        0       15        53         5
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(20Q12) MUTATED           3        19         17         67
  AMP PEAK 26(20Q12) WILD-TYPE         0         7          1         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 26(20Q12) MUTATED           44       56        24         1
  AMP PEAK 26(20Q12) WILD-TYPE         10        7         2         1
D26V4, multiclass
            clus
vv           AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  STAGE I                            79                           25
  STAGE IA                            1                            0
  STAGE II                           21                           15
  STAGE IIA                         120                           53
  STAGE IIB                           5                            5
  STAGE IIC                           3                            0
  STAGE III                          19                            7
  STAGE IIIA                         17                            1
  STAGE IIIB                         67                           16
  STAGE IIIC                         44                           10
  STAGE IV                           56                            7
  STAGE IVA                          24                            2
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 26(20Q12) MUTATED    14  85 321  46
  AMP PEAK 26(20Q12) WILD-TYPE   6  21  96  21
D26V5, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  T1                         14                            6
  T2                         85                           21
  T3                        321                           96
  T4                         46                           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 26(20Q12) MUTATED   244 129  93
  AMP PEAK 26(20Q12) WILD-TYPE 101  21  22
D26V6, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  N0                        244                          101
  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"
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   333  79
  AMP PEAK 26(20Q12) WILD-TYPE 117   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    333   79
  AMP PEAK 26(20Q12) WILD-TYPE  117    9
   clus
vv  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  0                        333                          117
  1                         79                            9
[1] 2 2
[1] FALSE
D26V8, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   213 255
  AMP PEAK 26(20Q12) WILD-TYPE  74  70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    213  255
  AMP PEAK 26(20Q12) WILD-TYPE   74   70
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  FEMALE                        213                           74
  MALE                          255                           70
[1] 2 2
[1] FALSE
D26V9, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   333  24
  AMP PEAK 26(20Q12) WILD-TYPE 113   4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    333   24
  AMP PEAK 26(20Q12) WILD-TYPE  113    4
     clus
vv    AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  NO                         333                          113
  YES                         24                            4
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                    293
  AMP PEAK 26(20Q12) WILD-TYPE                   89
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                              24
  AMP PEAK 26(20Q12) WILD-TYPE                            36
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                     136
  AMP PEAK 26(20Q12) WILD-TYPE                    10
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                                7
  AMP PEAK 26(20Q12) WILD-TYPE                              6
D26V10, multiclass
                                clus
vv                               AMP PEAK 26(20Q12) MUTATED
  COLON ADENOCARCINOMA                                  293
  COLON MUCINOUS ADENOCARCINOMA                          24
  RECTAL ADENOCARCINOMA                                 136
  RECTAL MUCINOUS ADENOCARCINOMA                          7
                                clus
vv                               AMP PEAK 26(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                     89
  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 26(20Q12) MUTATED   336   4  32  17
  AMP PEAK 26(20Q12) WILD-TYPE 106   1   5  12
D26V11, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  R0                        336                          106
  R1                          4                            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"
D26V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(20Q12) MUTATED                                  1     7
  AMP PEAK 26(20Q12) WILD-TYPE                                0     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(20Q12) MUTATED                          47   232
  AMP PEAK 26(20Q12) WILD-TYPE                        17    60
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                47
  WHITE                                                   232
                                  clus
vv                                 AMP PEAK 26(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED     4 269
  AMP PEAK 26(20Q12) WILD-TYPE   1  79
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED      4  269
  AMP PEAK 26(20Q12) WILD-TYPE    1   79
                        clus
vv                       AMP PEAK 26(20Q12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        269
                        clus
vv                       AMP PEAK 26(20Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           79
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q13.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q13.31) MUTATED   366  89
  AMP PEAK 27(20Q13.31) WILD-TYPE 106  32
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            455                             138 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                             89                              32 
$`AMP PEAK 27(20Q13.31) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.45        32.91        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.16        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-3494 
       61.84        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05         1.02        58.03         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
        9.07        36.03        19.07         0.00        19.07        34.03 
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-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       14.93         0.00        17.03        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99         1.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        15.52         0.79         0.72         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-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       33.01        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
       12.20        14.30        17.56       148.01        85.45        49.08 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
        9.99         1.91        20.02        37.02        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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02         2.96 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        17.75        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.80        17.13        12.49         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        4.41        12.43        14.30         9.04        11.64         4.80 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       35.97       117.07        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18         1.55        34.42        41.42        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 
       33.67        13.25         0.53        47.41       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        8.35        82.39        23.51        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       26.43        26.04        13.78        91.79        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       18.18        19.33        15.65        12.79        17.85        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        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 
       10.39        86.63        65.98        11.84        36.03         8.02 
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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
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-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        46.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 27(20Q13.31) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
       12.66         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       31.63        33.53        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-3502 
       20.12        19.66        16.24        24.92         3.02        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       63.98        13.02         1.02        24.03        37.05         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 
        0.99        17.95        29.95        61.02         6.97         0.92 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
       11.01        26.99        19.04        19.04         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 
       15.95         0.00         0.00        36.03        53.00        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R 
       25.02        27.02        38.04        30.02        18.05         0.99 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       34.98        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
       22.03        18.05        56.55        10.88         0.20         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       27.09        21.44        17.82        75.95        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 
       32.94        88.21         6.77       100.01         3.25        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         1.51        12.00       140.38       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 
       81.37        60.79        98.24        11.11        47.87        35.31 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       67.30        53.62        85.48        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-T9-A92H 
       79.69        10.98        19.33         9.93        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       70.03        34.49        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 
       32.98        19.04        13.02         3.98        20.98        49.97 
TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       61.97         5.29        19.96         8.61        17.46         8.45 

  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                              0                               0 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                         19.990                          21.735 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (21.7)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   321 145
  AMP PEAK 27(20Q13.31) WILD-TYPE 125  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    321  145
  AMP PEAK 27(20Q13.31) WILD-TYPE  125   17
        clus
vv       AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  COLON                            321                             125
  RECTUM                           145                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 27(20Q13.31) MUTATED        79        1       22       120         5
  AMP PEAK 27(20Q13.31) WILD-TYPE      25        0       14        53         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(20Q13.31) MUTATED           3        20         17         67
  AMP PEAK 27(20Q13.31) WILD-TYPE         0         6          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 27(20Q13.31) MUTATED           45       57        23         1
  AMP PEAK 27(20Q13.31) WILD-TYPE          9        6         3         1
D27V4, multiclass
            clus
vv           AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  STAGE I                               79                              25
  STAGE IA                               1                               0
  STAGE II                              22                              14
  STAGE IIA                            120                              53
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             20                               6
  STAGE IIIA                            17                               1
  STAGE IIIB                            67                              16
  STAGE IIIC                            45                               9
  STAGE IV                              57                               6
  STAGE IVA                             23                               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 27(20Q13.31) MUTATED    14  85 324  45
  AMP PEAK 27(20Q13.31) WILD-TYPE   6  21  93  22
D27V5, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  T1                            14                               6
  T2                            85                              21
  T3                           324                              93
  T4                            45                              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 27(20Q13.31) MUTATED   245 129  94
  AMP PEAK 27(20Q13.31) WILD-TYPE 100  21  21
D27V6, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  N0                           245                             100
  N1                           129                              21
  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"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   336  79
  AMP PEAK 27(20Q13.31) WILD-TYPE 114   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    336   79
  AMP PEAK 27(20Q13.31) WILD-TYPE  114    9
   clus
vv  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  0                           336                             114
  1                            79                               9
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   216 254
  AMP PEAK 27(20Q13.31) WILD-TYPE  71  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    216  254
  AMP PEAK 27(20Q13.31) WILD-TYPE   71   71
        clus
vv       AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  FEMALE                           216                              71
  MALE                             254                              71
[1] 2 2
[1] FALSE
D27V9, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   336  24
  AMP PEAK 27(20Q13.31) WILD-TYPE 110   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    336   24
  AMP PEAK 27(20Q13.31) WILD-TYPE  110    4
     clus
vv    AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  NO                            336                             110
  YES                            24                               4
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                    293
  AMP PEAK 27(20Q13.31) WILD-TYPE                   89
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                              25
  AMP PEAK 27(20Q13.31) WILD-TYPE                            35
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                     136
  AMP PEAK 27(20Q13.31) WILD-TYPE                    10
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                                7
  AMP PEAK 27(20Q13.31) WILD-TYPE                              6
D27V10, multiclass
                                clus
vv                               AMP PEAK 27(20Q13.31) MUTATED
  COLON ADENOCARCINOMA                                     293
  COLON MUCINOUS ADENOCARCINOMA                             25
  RECTAL ADENOCARCINOMA                                    136
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 27(20Q13.31) WILD-TYPE
  COLON ADENOCARCINOMA                                        89
  COLON MUCINOUS ADENOCARCINOMA                               35
  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 27(20Q13.31) MUTATED   338   4  32  17
  AMP PEAK 27(20Q13.31) WILD-TYPE 104   1   5  12
D27V11, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  R0                           338                             104
  R1                             4                               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"
D27V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(20Q13.31) MUTATED                                  1     7
  AMP PEAK 27(20Q13.31) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.31) MUTATED                          46   232
  AMP PEAK 27(20Q13.31) WILD-TYPE                        18    60
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   46
  WHITE                                                      232
                                  clus
vv                                 AMP PEAK 27(20Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     18
  WHITE                                                         60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED     4 269
  AMP PEAK 27(20Q13.31) WILD-TYPE   1  79
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED      4  269
  AMP PEAK 27(20Q13.31) WILD-TYPE    1   79
                        clus
vv                       AMP PEAK 27(20Q13.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           269
                        clus
vv                       AMP PEAK 27(20Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              79
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   179  54
  DEL PEAK  1(1P36.11) WILD-TYPE 293  67
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           233                            360 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            54                             67 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 
        4.80         1.61        43.76        24.33        44.91        35.11 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 
       13.94        16.57        36.53        14.53        32.45        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       23.61        32.71        29.16        22.52        24.13        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       21.76        23.87        56.25         5.03        38.99         9.07 
TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3552 
       37.05        19.07        19.07        34.03        14.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       24.00        23.01        19.99         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 
       47.01        37.05        19.00        36.00        85.05        10.06 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       25.02        38.99        36.95        37.02        10.06        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 
       29.98         2.01        12.99         2.01         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       50.99        13.05        26.01         7.96        34.03        42.02 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
        1.02        15.02        32.02        31.00        33.04        26.01 
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-6965 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         5.79        22.42         0.20        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 
       14.50        16.31        17.85         5.65         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       65.00        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07        12.20        14.30 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
        9.99         1.91        25.02         8.02        13.02        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       30.08         5.03        15.02         2.96        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       15.02        11.01        11.08        10.06        12.03        45.40 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.19        17.75         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 
       17.85        15.58        12.43        14.30         4.80        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       92.75        49.91        44.32       139.17         6.12        26.47 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 
      117.07        95.18        31.96        11.11         1.55        41.42 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       13.25        47.41         8.35        82.39        23.51        65.85 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       35.93        61.91        36.00        91.79        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-T9-A92H TCGA-AF-2687 
       10.98         9.93        16.80        42.77        11.90        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        13.55        19.10        10.39        14.50 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       15.39        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-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       36.95        17.03         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       36.03        13.94        25.97        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       64.01        51.98         1.94        38.96        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 
        0.69         0.72        10.19         6.97         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
        5.03         8.98        13.97        15.02        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
        5.95         5.03       126.44       129.27        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 
        2.40        20.55        15.85        11.97         8.45        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       32.19         0.69        12.46        47.08        26.43 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       15.62        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       43.43        42.90        42.28        45.60        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       37.02        34.65        32.91        31.63        30.44        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.09        22.06        27.09         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84         9.63         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        6.97         1.02        13.02         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        8.05         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
        0.99        33.99        21.01        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       54.02         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
        0.00         0.00        36.03        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       34.03        16.08        34.06        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        34.98        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        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        10.88         0.92        27.09         0.95        33.01 
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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5403 
       75.95        58.39         1.41        32.94       106.75        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       88.21        49.41         6.77       100.01        11.74         1.61 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        49.08        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        12.26 
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         1.48         3.68         4.41         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C 
        7.50       131.51       135.65         7.76        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 
      119.93        35.97        60.79        98.24         8.61        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        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        35.31       133.18        28.21        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        79.69        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       17.85        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       30.28        70.03        39.48        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        36.03        12.00         8.02         7.07 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
       32.98         0.99         0.99        17.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       14.01        32.02        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       46.03        20.98         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
        9.07         1.02        31.00        10.98        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       41.00         1.45        26.43         1.81         6.05        33.17 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        9.37        12.39        78.12         7.17        21.01        15.02 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.98         4.01         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       51.48        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       13.64        17.46         9.96        49.51        31.30         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.53         1.12         0.76        18.28        55.76 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           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 
                         19.99                          20.20 
[1] "0.1 - 139.2 (20.0)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   166  73
  DEL PEAK  1(1P36.11) WILD-TYPE 280  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    166   73
  DEL PEAK  1(1P36.11) WILD-TYPE  280   89
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  COLON                           166                            280
  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        8        63         3
  DEL PEAK  1(1P36.11) WILD-TYPE      71        1       28       110         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1        10          7         31
  DEL PEAK  1(1P36.11) WILD-TYPE         2        16         11         52
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           25       38        16         0
  DEL PEAK  1(1P36.11) WILD-TYPE         29       25        10         2
D28V4, 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                              8                             28
  STAGE IIA                            63                            110
  STAGE IIB                             3                              7
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            7                             11
  STAGE IIIB                           31                             52
  STAGE IIIC                           25                             29
  STAGE IV                             38                             25
  STAGE IVA                            16                             10
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED     5  40 164  32
  DEL PEAK  1(1P36.11) WILD-TYPE  15  66 253  35
D28V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            5                             15
  T2                           40                             66
  T3                          164                            253
  T4                           32                             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  1(1P36.11) MUTATED   117  65  58
  DEL PEAK  1(1P36.11) WILD-TYPE 228  85  57
D28V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          117                            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"
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   162  53
  DEL PEAK  1(1P36.11) WILD-TYPE 288  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    162   53
  DEL PEAK  1(1P36.11) WILD-TYPE  288   35
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          162                            288
  1                           53                             35
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   104 138
  DEL PEAK  1(1P36.11) WILD-TYPE 183 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    104  138
  DEL PEAK  1(1P36.11) WILD-TYPE  183  187
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                          104                            183
  MALE                            138                            187
[1] 2 2
[1] FALSE
D28V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   170  13
  DEL PEAK  1(1P36.11) WILD-TYPE 276  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    170   13
  DEL PEAK  1(1P36.11) WILD-TYPE  276   15
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           170                            276
  YES                           13                             15
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                    154
  DEL PEAK  1(1P36.11) WILD-TYPE                  228
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              11
  DEL PEAK  1(1P36.11) WILD-TYPE                            49
                                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
D28V10, multiclass
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                    154
  COLON MUCINOUS ADENOCARCINOMA                            11
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      228
  COLON MUCINOUS ADENOCARCINOMA                              49
  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   165   2  21  12
  DEL PEAK  1(1P36.11) WILD-TYPE 277   3  16  17
D28V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          165                            277
  R1                            2                              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"
D28V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.11) MUTATED                                  1     7
  DEL PEAK  1(1P36.11) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                          24   115
  DEL PEAK  1(1P36.11) WILD-TYPE                        40   177
D28V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  24
  WHITE                                                     115
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     2 136
  DEL PEAK  1(1P36.11) WILD-TYPE   3 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      2  136
  DEL PEAK  1(1P36.11) WILD-TYPE    3  212
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            212
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED   126  43
  DEL PEAK  2(1P33) WILD-TYPE 346  78
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        169                         424 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         43                          78 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
        4.80         1.61        43.76        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 
       37.02        36.53        14.53        32.45        29.19        23.61 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 
       29.16        22.52        21.76        23.87         5.03        38.99 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3562 TCGA-AA-3673 
        9.07        37.05         8.05        21.01        19.99        50.04 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 
       37.05        19.00        85.05        10.06        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 
       37.02         0.00        10.06        33.07        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       17.03        24.03         2.01        12.99         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F 
       13.05         7.96        34.03        42.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R 
       31.00        33.04        26.01         2.96         2.01        22.03 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00         0.79         5.79        22.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 
       14.50        16.31        17.85         5.65         5.13        62.79 
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         3.06 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
        2.14        12.20         1.91         8.02        13.02        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        5.03        15.02         2.96        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 
       11.08        11.08        10.06        56.09         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 
       17.85        14.30         4.80        11.38        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 
       49.91        14.04        26.47        35.97        31.96         1.55 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 
       47.41         8.35        82.39        23.51        65.85        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       61.91        36.00        91.79        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
        9.93        16.80        42.77        11.90        24.13        17.23 
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       13.55        14.50        15.39        86.63        65.98        11.84 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 
       32.02        36.03        24.00        34.03        29.98        37.02 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       19.04        19.99         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 
       36.03        25.97        23.01        12.00        70.03         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 
       38.96        38.04        38.56         0.69        10.19         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
        4.73        12.39        21.01        11.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 
       27.95        19.99       126.44       129.27         0.49        20.55 
TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       15.85        13.64        11.97        28.57        32.19         0.69 
TCGA-G5-6572 
       47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       15.62        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 
       43.43        42.90        24.33        42.28        44.91        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       13.94        37.05        34.65        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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 
        1.02        13.02         1.02        24.03        36.03        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.00         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        1.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         5.03         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37        15.52        56.55         0.72        27.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       10.88         0.46         0.92        27.09         0.95        33.01 
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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       75.95        58.39         1.41        32.94       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       65.00        88.21        49.41         6.77       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        1.61         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        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-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-6678 
       12.99        14.04        11.01        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        19.59        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-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         1.48         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26       119.70        24.43       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17         6.12        81.37       119.93        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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 
       13.25         0.53        35.31       133.18        28.21        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       39.42        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       26.17        74.79        79.69        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        17.85        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       21.90        30.28        70.03        39.48        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        10.39        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       36.03        12.00         8.02         7.07        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 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-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        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-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       14.01        32.02        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
       46.03        20.98        13.94         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07         1.02        31.00        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
       51.98        49.97        61.97        41.00         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
       26.43         1.81         6.05        33.17         6.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
        7.17        15.02         8.98        15.02        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        17.69        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-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       31.30         0.39         0.66         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       12.46        18.28        55.76        26.43 

  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 
                      19.99                       20.02 
[1] "0.0 - 129.3 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   122  51
  DEL PEAK  2(1P33) WILD-TYPE 324 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    122   51
  DEL PEAK  2(1P33) WILD-TYPE  324  111
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  COLON                        122                         324
  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        7        50         1
  DEL PEAK  2(1P33) WILD-TYPE      85        1       29       123         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         7          5         25
  DEL PEAK  2(1P33) WILD-TYPE         3        19         13         58
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           20       29         6         0
  DEL PEAK  2(1P33) WILD-TYPE         34       34        20         2
D29V4, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           19                          85
  STAGE IA                           0                           1
  STAGE II                           7                          29
  STAGE IIA                         50                         123
  STAGE IIB                          1                           9
  STAGE IIC                          0                           3
  STAGE III                          7                          19
  STAGE IIIA                         5                          13
  STAGE IIIB                        25                          58
  STAGE IIIC                        20                          34
  STAGE IV                          29                          34
  STAGE IVA                          6                          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  2(1P33) MUTATED     4  23 126  21
  DEL PEAK  2(1P33) WILD-TYPE  16  83 291  46
D29V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         4                          16
  T2                        23                          83
  T3                       126                         291
  T4                        21                          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  2(1P33) MUTATED    84  51  39
  DEL PEAK  2(1P33) WILD-TYPE 261  99  76
D29V6, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        84                         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"
D29V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   118  35
  DEL PEAK  2(1P33) WILD-TYPE 332  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    118   35
  DEL PEAK  2(1P33) WILD-TYPE  332   53
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                       118                         332
  1                        35                          53
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    78  97
  DEL PEAK  2(1P33) WILD-TYPE 209 228
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     78   97
  DEL PEAK  2(1P33) WILD-TYPE  209  228
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        78                         209
  MALE                          97                         228
[1] 2 2
[1] FALSE
D29V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   127  10
  DEL PEAK  2(1P33) WILD-TYPE 319  18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    127   10
  DEL PEAK  2(1P33) WILD-TYPE  319   18
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                        127                         319
  YES                        10                          18
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                    112
  DEL PEAK  2(1P33) WILD-TYPE                  270
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                               9
  DEL PEAK  2(1P33) WILD-TYPE                            51
                             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
D29V10, multiclass
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                 112
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 49
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                   270
  COLON MUCINOUS ADENOCARCINOMA                           51
  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   116   2  14   8
  DEL PEAK  2(1P33) WILD-TYPE 326   3  23  21
D29V11, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                       116                         326
  R1                         2                           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"
D29V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P33) MUTATED                                  1     4
  DEL PEAK  2(1P33) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED                          23    83
  DEL PEAK  2(1P33) WILD-TYPE                        41   209
D29V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               23
  WHITE                                                   83
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 41
  WHITE                                                    209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     3 101
  DEL PEAK  2(1P33) WILD-TYPE   2 247
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3  101
  DEL PEAK  2(1P33) WILD-TYPE    2  247
                        clus
vv                       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  HISPANIC OR LATINO                             3                           2
  NOT HISPANIC OR LATINO                       101                         247
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.2) MUTATED   127  42
  DEL PEAK  3(1P13.2) WILD-TYPE 345  79
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          169                           424 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           42                            79 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 
        4.80         1.61        43.76        43.76        35.11        16.57 
TCGA-A6-2685 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 
       37.25        36.53        14.53        32.45        29.19        23.61 
TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 
       22.52        21.76        23.87        56.25         5.03        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 
        9.07        24.03        37.05        21.01        13.94        19.99 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 
       50.04        37.05        19.00        10.06        38.99        37.02 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 
       10.06        32.05        31.07        17.03        24.03         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 
       12.99         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 
        0.79         5.79        22.42         0.20        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         3.06 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
        2.14        12.20         1.91         8.02        13.02        22.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 
        2.96        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         1.32        15.12        14.30         4.80 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 
       11.38        92.75        49.91       131.51         6.12        14.04 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
       26.47        31.96         1.55        16.24        33.67        47.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
        8.35        82.39        23.51        65.85        61.91        36.00 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 
       91.79        46.75        18.18        10.98         9.93        16.80 
TCGA-QG-A5YV TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 
       42.77        11.90        24.13        17.23        13.55        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       15.39        65.98        11.84        32.02        36.03        24.00 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 
       34.03         2.01        29.98        37.02        19.04        19.99 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00H 
        1.02        19.99        28.04        36.03         3.98        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 
       23.01        12.00        70.03         1.94        38.04        38.56 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
        0.69        10.19         9.37        11.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 
       27.95        19.99       126.44        41.36       129.27         0.49 
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-G5-6233 
       28.57        32.19         0.66         0.69         0.76        18.28 
TCGA-G5-6572 
       47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2675 
       15.62        12.66         9.53        39.45        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        42.28        44.91        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.05        37.02        34.65        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       17.95        29.95        23.01        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
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-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       36.95        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       29.98        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       24.00        20.98        34.03        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05         0.07        21.37        15.52        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.46        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
      109.28        75.95        58.39         1.41       106.75        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        1.61         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        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-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        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-6165 
       15.02        15.02        17.03        15.02        12.00        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-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       19.59        55.92        20.19        20.42        18.25        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 
        1.48         3.68         4.41        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       44.32       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-G4-6294 
       41.42        13.25         0.53        35.31       133.18        28.21 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       63.62        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       13.78        35.80        26.17        74.79        79.69        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        15.65        12.79        17.85        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        30.28        70.03        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        19.10        34.49        37.74        10.39        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        10.39        86.63        36.03        12.00         8.02 
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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       13.94        19.99        20.98         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 
       13.02        35.01        14.01        48.03        32.02        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03        46.03        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         1.45         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       33.17         6.97         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       21.01        15.02         8.98        15.02        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         5.03         5.29        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
       32.61         2.40        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.31        16.41         8.61        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 
        8.45         9.96        49.51        31.30         0.39         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        1.12        12.46        55.76        26.43 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          0.2                           0.0 
  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 
                        18.18                         20.35 
[1] "0.2 - 131.5 (18.2)" "0.0 - 148.0 (20.4)"
[1] "hr=" "1.5"
D30V2, continuous
D30V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   120  52
  DEL PEAK  3(1P13.2) WILD-TYPE 326 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    120   52
  DEL PEAK  3(1P13.2) WILD-TYPE  326  110
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  COLON                          120                           326
  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         1
  DEL PEAK  3(1P13.2) WILD-TYPE      85        1       28       125         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.2) MUTATED           2         5          4         24
  DEL PEAK  3(1P13.2) WILD-TYPE         1        21         14         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.2) MUTATED           21       30         6         0
  DEL PEAK  3(1P13.2) WILD-TYPE         33       33        20         2
D30V4, 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                            28
  STAGE IIA                           48                           125
  STAGE IIB                            1                             9
  STAGE IIC                            2                             1
  STAGE III                            5                            21
  STAGE IIIA                           4                            14
  STAGE IIIB                          24                            59
  STAGE IIIC                          21                            33
  STAGE IV                            30                            33
  STAGE IVA                            6                            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  3(1P13.2) MUTATED     5  21 125  22
  DEL PEAK  3(1P13.2) WILD-TYPE  15  85 292  45
D30V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           5                            15
  T2                          21                            85
  T3                         125                           292
  T4                          22                            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  3(1P13.2) MUTATED    83  46  44
  DEL PEAK  3(1P13.2) WILD-TYPE 262 104  71
D30V6, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          83                           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"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   119  36
  DEL PEAK  3(1P13.2) WILD-TYPE 331  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    119   36
  DEL PEAK  3(1P13.2) WILD-TYPE  331   52
   clus
vv  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  0                         119                           331
  1                          36                            52
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED    77  97
  DEL PEAK  3(1P13.2) WILD-TYPE 210 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     77   97
  DEL PEAK  3(1P13.2) WILD-TYPE  210  228
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          77                           210
  MALE                            97                           228
[1] 2 2
[1] FALSE
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   124  10
  DEL PEAK  3(1P13.2) WILD-TYPE 322  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    124   10
  DEL PEAK  3(1P13.2) WILD-TYPE  322   18
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                          124                           322
  YES                          10                            18
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                    110
  DEL PEAK  3(1P13.2) WILD-TYPE                  272
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                              10
  DEL PEAK  3(1P13.2) WILD-TYPE                            50
                               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
D30V10, multiclass
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  COLON ADENOCARCINOMA                                   110
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     272
  COLON MUCINOUS ADENOCARCINOMA                             50
  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   117   1  14   9
  DEL PEAK  3(1P13.2) WILD-TYPE 325   4  23  20
D30V11, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                         117                           325
  R1                           1                             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"
D30V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1P13.2) MUTATED                                  1     4
  DEL PEAK  3(1P13.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.2) MUTATED                          22    85
  DEL PEAK  3(1P13.2) WILD-TYPE                        42   207
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                     85
                                  clus
vv                                 DEL PEAK  3(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     2 102
  DEL PEAK  3(1P13.2) WILD-TYPE   3 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      2  102
  DEL PEAK  3(1P13.2) WILD-TYPE    3  246
                        clus
vv                       DEL PEAK  3(1P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         102
                        clus
vv                       DEL PEAK  3(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           246
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    18   3
  DEL PEAK  4(2P12) WILD-TYPE 454 118
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         572 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          3                         118 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-A6-2677 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 TCGA-AA-A01S 
       24.33         6.97        19.99        37.02        12.99         1.02 
TCGA-CM-5341 TCGA-G4-6626 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       29.06        46.75        15.39        32.02        36.03         6.05 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-A00H 
       19.99        13.94        19.04         1.02        28.04        25.97 
TCGA-AG-A02X TCGA-DC-6156 TCGA-F5-6571 
       41.00        15.02        31.30 

$`DEL PEAK  4(2P12) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        14.93         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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
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-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         5.79        22.42        27.42        10.88         0.20 
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-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       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-5344 
       25.02        26.04         8.02        27.02        13.02        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         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
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-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        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         1.48         3.68         4.41 
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         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       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        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        47.41        35.31       133.18        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       61.91        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        74.79        79.69        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-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        30.28        11.90        70.03        24.13 
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        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        16.83        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       86.63        65.98        11.84        36.03        12.00         8.02 
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-3592 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-3612 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-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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-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-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        8.98        13.97        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  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 
                      19.99                       19.99 
[1] "1.0 - 46.8 (20.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8  13
  DEL PEAK  4(2P12) WILD-TYPE 438 149
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   13
  DEL PEAK  4(2P12) WILD-TYPE  438  149
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  COLON                          8                         438
  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       35       166        10
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2P12) MUTATED           0         1          2          1
  DEL PEAK  4(2P12) WILD-TYPE         3        25         16         82
                             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         49       62        25         2
D31V4, 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                          35
  STAGE IIA                          7                         166
  STAGE IIB                          0                          10
  STAGE IIC                          0                           3
  STAGE III                          1                          25
  STAGE IIIA                         2                          16
  STAGE IIIB                         1                          82
  STAGE IIIC                         5                          49
  STAGE IV                           1                          62
  STAGE IVA                          1                          25
  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  20 102 402  65
D31V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                          20
  T2                         4                         102
  T3                        15                         402
  T4                         2                          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  4(2P12) MUTATED    10   5   6
  DEL PEAK  4(2P12) WILD-TYPE 335 145 109
D31V6, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        10                         335
  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"
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    18   2
  DEL PEAK  4(2P12) WILD-TYPE 432  86
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     18    2
  DEL PEAK  4(2P12) WILD-TYPE  432   86
   clus
vv  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  0                        18                         432
  1                         2                          86
[1] 2 2
[1] FALSE
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11  10
  DEL PEAK  4(2P12) WILD-TYPE 276 315
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11   10
  DEL PEAK  4(2P12) WILD-TYPE  276  315
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                        11                         276
  MALE                          10                         315
[1] 2 2
[1] FALSE
D31V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    15   3
  DEL PEAK  4(2P12) WILD-TYPE 431  25
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     15    3
  DEL PEAK  4(2P12) WILD-TYPE  431   25
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                         15                         431
  YES                         3                          25
[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                            60
                             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
D31V10, 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                           60
  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 424   5  36  29
D31V11, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        18                         424
  R1                         0                           5
  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"
D31V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2P12) MUTATED                                  0     0
  DEL PEAK  4(2P12) WILD-TYPE                                1    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P12) MUTATED                           0     6
  DEL PEAK  4(2P12) WILD-TYPE                        64   286
D31V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  4(2P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     12
  BLACK OR AFRICAN AMERICAN                                 64
  WHITE                                                    286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     0   6
  DEL PEAK  4(2P12) WILD-TYPE   5 342
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      0    6
  DEL PEAK  4(2P12) WILD-TYPE    5  342
                        clus
vv                       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                         6                         342
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    27   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 445 114
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           34                           559 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                           114 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3522 
       42.28        36.53        21.76        24.92         6.97        37.05 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3848 
       19.99         2.01        15.02        10.06        37.02        10.06 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AZ-4308 TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 
       12.99        24.00       109.28        12.69         3.29        49.91 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6626 TCGA-AF-A56L 
       44.32       131.51       117.07         1.55        46.75        65.98 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A014 
       19.99        13.94        19.04        36.03        25.97        15.95 
TCGA-AG-A02X TCGA-DC-6682 TCGA-F5-6571 TCGA-F5-6814 
       41.00         4.01        31.30         0.53 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        36.95        14.93         0.00        17.03         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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98         1.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-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         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19         1.61         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       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-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-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 
        2.96        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 
       12.26        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         1.32        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         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        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         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38         7.50       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-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 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        17.85        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        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       16.83        15.39        20.02        10.39        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        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-3612 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-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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-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-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         0.53                          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 
                        22.88                         19.99 
[1] "0.5 - 131.5 (22.9)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.2"
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    24  11
  DEL PEAK  5(2Q22.1) WILD-TYPE 422 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     24   11
  DEL PEAK  5(2Q22.1) WILD-TYPE  422  151
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON                           24                           422
  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       35       158        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q22.1) MUTATED           0         2          1          4
  DEL PEAK  5(2Q22.1) WILD-TYPE         3        24         17         79
                               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         47       61        25         2
D32V4, 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                            35
  STAGE IIA                           15                           158
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           1                            17
  STAGE IIIB                           4                            79
  STAGE IIIC                           7                            47
  STAGE IV                             2                            61
  STAGE IVA                            1                            25
  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   4  27   4
  DEL PEAK  5(2Q22.1) WILD-TYPE  20 102 390  63
D32V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           102
  T3                          27                           390
  T4                           4                            63
[1] 4 2
[1] TRUE
[1] "dimension 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 327 142 106
D32V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          18                           327
  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"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    30   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 420  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     30    3
  DEL PEAK  5(2Q22.1) WILD-TYPE  420   85
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          30                           420
  1                           3                            85
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    15  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 272 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     15   20
  DEL PEAK  5(2Q22.1) WILD-TYPE  272  305
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          15                           272
  MALE                            20                           305
[1] 2 2
[1] FALSE
D32V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    23   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 423  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     23    1
  DEL PEAK  5(2Q22.1) WILD-TYPE  423   27
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           23                           423
  YES                           1                            27
[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                            57
                               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
D32V10, 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                             57
  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 417   5  35  27
D32V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          25                           417
  R1                           0                             5
  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"
D32V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q22.1) MUTATED                                  1     2
  DEL PEAK  5(2Q22.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q22.1) MUTATED                           2    12
  DEL PEAK  5(2Q22.1) WILD-TYPE                        62   280
D32V13, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     12
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   62
  WHITE                                                      280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  16
  DEL PEAK  5(2Q22.1) WILD-TYPE   5 332
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   16
  DEL PEAK  5(2Q22.1) WILD-TYPE    5  332
                        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                           332
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  6(3P26.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.3) MUTATED    69  21
  DEL PEAK  6(3P26.3) WILD-TYPE 403 100
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           90                           503 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           21                           100 
$`DEL PEAK  6(3P26.3) MUTATED`
TCGA-5M-AAT4 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
        1.61        43.43        16.57        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU 
       32.45        29.16        22.52        25.08        21.76         9.63 
TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3662 
        5.03         6.97        38.99         9.07        29.00         6.05 
TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 
       15.02        85.05        10.06        32.05        31.07        17.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 
       29.98         2.01        12.99         2.01         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F 
       50.99        24.00         7.96        13.94        27.02        32.02 
TCGA-AA-A01K TCGA-AA-A02H TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 
       31.00         2.01        16.44         5.65         5.13        12.10 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
        3.19         3.29        12.20         1.91         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 
       29.06        22.03         5.03         2.96        11.08        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        17.75         1.32        43.27        15.12        17.85 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV 
        4.80        11.38         7.50        31.96         9.93        42.77 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 
       30.28        11.90        13.55        34.49        14.50        20.05 
TCGA-AG-3584 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       24.00         0.99        37.02        19.04        19.99        17.95 
TCGA-AG-4021 TCGA-AG-A02N TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 
        3.98        61.97        38.56        10.19         6.05         4.73 
TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6810 TCGA-G5-6233 
        4.01         5.29        17.69        16.31         0.39        18.28 

$`DEL PEAK  6(3P26.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        37.05        37.25        37.02 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       56.25         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         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-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        24.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       34.03        18.05        18.05        38.04         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88         0.20         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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       75.95        58.39         1.41        32.94       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.14         3.25         0.07        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32         9.99        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-5348 
       20.02        37.02        25.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 
       19.59        56.09        55.92        20.42        18.25         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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        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-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 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 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        15.65        12.79        17.85        16.80        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        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       39.48        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       36.03         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-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
       19.99        13.94        19.99        20.98         7.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99         0.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.94        38.96        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81        33.17         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.95         5.03       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        55.76        47.08        26.43 

  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                         0.39                          0.00 
  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 
                        15.07                         20.98 
[1] "0.4 - 85.0 (15.1)"  "0.0 - 148.0 (21.0)"
[1] "hr=" "1.8"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    70  20
  DEL PEAK  6(3P26.3) WILD-TYPE 376 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     70   20
  DEL PEAK  6(3P26.3) WILD-TYPE  376  142
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  COLON                           70                           376
  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        3        25         0
  DEL PEAK  6(3P26.3) WILD-TYPE      96        1       33       148        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.3) MUTATED           1         5          2         14
  DEL PEAK  6(3P26.3) WILD-TYPE         2        21         16         69
                               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         46       43        21         2
D33V4, 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                             3                            33
  STAGE IIA                           25                           148
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           2                            16
  STAGE IIIB                          14                            69
  STAGE IIIC                           8                            46
  STAGE IV                            20                            43
  STAGE IVA                            5                            21
  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  71  11
  DEL PEAK  6(3P26.3) WILD-TYPE  18  98 346  56
D33V5, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  T1                           2                            18
  T2                           8                            98
  T3                          71                           346
  T4                          11                            56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  6(3P26.3) MUTATED    40  28  24
  DEL PEAK  6(3P26.3) WILD-TYPE 305 122  91
D33V6, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  N0                          40                           305
  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"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    56  25
  DEL PEAK  6(3P26.3) WILD-TYPE 394  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     56   25
  DEL PEAK  6(3P26.3) WILD-TYPE  394   63
   clus
vv  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  0                          56                           394
  1                          25                            63
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    40  52
  DEL PEAK  6(3P26.3) WILD-TYPE 247 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     40   52
  DEL PEAK  6(3P26.3) WILD-TYPE  247  273
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  FEMALE                          40                           247
  MALE                            52                           273
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    72   3
  DEL PEAK  6(3P26.3) WILD-TYPE 374  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     72    3
  DEL PEAK  6(3P26.3) WILD-TYPE  374   25
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  NO                           72                           374
  YES                           3                            25
[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                            56
                               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
D33V10, 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                             56
  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 379   5  26  24
D33V11, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  R0                          63                           379
  R1                           0                             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"
D33V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3P26.3) MUTATED                                  0     3
  DEL PEAK  6(3P26.3) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P26.3) MUTATED                           9    44
  DEL PEAK  6(3P26.3) WILD-TYPE                        55   248
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  6(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     44
                                  clus
vv                                 DEL PEAK  6(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      248
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED     2  53
  DEL PEAK  6(3P26.3) WILD-TYPE   3 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED      2   53
  DEL PEAK  6(3P26.3) WILD-TYPE    3  295
                        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                           295
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  7(3P14.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.2) MUTATED    89  25
  DEL PEAK  7(3P14.2) WILD-TYPE 383  96
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          114                           479 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           25                            96 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       12.66         1.61        16.57        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       14.53        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-3662 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3685 
        9.07         6.05        54.02         0.92        11.01        37.05 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 
       85.05        10.06        32.05        31.07        17.03         2.01 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       12.99         2.01        21.99        24.00        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F 
       13.94        18.05        38.04        27.02         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A02W TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK 
       31.00        41.00        21.37         0.79         5.79        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-6600 
        0.46        14.50        16.31       109.28         5.65        12.10 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        3.29        12.20         1.91         8.02         5.03         2.96 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       14.04        13.05        11.08        11.01        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 
        1.32        43.27        17.85         4.80        11.38       119.70 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 TCGA-NH-A6GA 
        7.50        35.97       117.07        31.96        36.00         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 
       16.80        42.77        30.28        11.90        70.03        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3580 
       19.10        34.49        14.50        86.63        11.84         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3592 TCGA-AG-3731 TCGA-AG-3732 
        7.07        20.05        24.00        34.03        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       19.04        19.99        17.95         1.02        17.03         6.02 
TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5337 
       38.96        38.56        10.19         6.05         9.37        15.02 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 TCGA-F5-6810 TCGA-G5-6233 
       10.98         4.01         5.29        20.91         0.39        18.28 

$`DEL PEAK  7(3P14.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       15.62         4.80         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       43.76        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 
       35.11        45.60        13.94        37.05        37.25        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-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       24.16        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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        6.97         1.02        13.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02         5.98        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-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-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       36.03         0.99        31.07        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       29.98        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       13.05        34.06        26.01        25.02        19.07        27.02 
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-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02        17.03        14.99        21.99        34.98         1.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20         0.92        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-4313 
       17.82        17.26        17.85        19.33        18.84        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13       106.75        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       49.08        51.32         9.99        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-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-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.01        12.95        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        12.26        19.59        56.09        55.92        20.42 
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         1.48         3.68         4.41        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79        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 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       63.62        39.42        35.93        61.91        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        17.85        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       31.30        21.90        24.13        39.48        17.23        13.55 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        16.83        15.39        20.02        10.39 
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-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99         0.99        29.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H 
       14.04         3.98        46.03        20.98        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72        26.43         1.81        33.17         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
        5.03         8.98        13.97        15.02        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.95         5.03       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        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        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        55.76        47.08        26.43 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                         0.39                          0.00 
  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 
                       16.915                        20.980 
[1] "0.4 - 119.7 (16.9)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    87  29
  DEL PEAK  7(3P14.2) WILD-TYPE 359 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     87   29
  DEL PEAK  7(3P14.2) WILD-TYPE  359  133
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  COLON                           87                           359
  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        3        33         0
  DEL PEAK  7(3P14.2) WILD-TYPE      85        1       33       140        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.2) MUTATED           1         5          1         18
  DEL PEAK  7(3P14.2) WILD-TYPE         2        21         17         65
                               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         43       45        20         1
D34V4, 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                             3                            33
  STAGE IIA                           33                           140
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           1                            17
  STAGE IIIB                          18                            65
  STAGE IIIC                          11                            43
  STAGE IV                            18                            45
  STAGE IVA                            6                            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  7(3P14.2) MUTATED     7  15  80  16
  DEL PEAK  7(3P14.2) WILD-TYPE  13  91 337  51
D34V5, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                           7                            13
  T2                          15                            91
  T3                          80                           337
  T4                          16                            51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  7(3P14.2) MUTATED    60  31  27
  DEL PEAK  7(3P14.2) WILD-TYPE 285 119  88
D34V6, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                          60                           285
  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"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    77  25
  DEL PEAK  7(3P14.2) WILD-TYPE 373  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     77   25
  DEL PEAK  7(3P14.2) WILD-TYPE  373   63
   clus
vv  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  0                          77                           373
  1                          25                            63
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    51  67
  DEL PEAK  7(3P14.2) WILD-TYPE 236 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     51   67
  DEL PEAK  7(3P14.2) WILD-TYPE  236  258
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                          51                           236
  MALE                            67                           258
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    91   5
  DEL PEAK  7(3P14.2) WILD-TYPE 355  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     91    5
  DEL PEAK  7(3P14.2) WILD-TYPE  355   23
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  NO                           91                           355
  YES                           5                            23
[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                            51
                               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
D34V10, 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                             51
  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 360   4  26  24
D34V11, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  R0                          82                           360
  R1                           1                             4
  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"
D34V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P14.2) MUTATED                                  0     3
  DEL PEAK  7(3P14.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P14.2) MUTATED                          16    53
  DEL PEAK  7(3P14.2) WILD-TYPE                        48   239
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK  7(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED     1  68
  DEL PEAK  7(3P14.2) WILD-TYPE   4 280
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      1   68
  DEL PEAK  7(3P14.2) WILD-TYPE    4  280
                        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                           280
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  8(3Q26.31) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(3Q26.31) MUTATED    50  13
  DEL PEAK  8(3Q26.31) WILD-TYPE 422 108
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            63                            530 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            13                            108 
$`DEL PEAK  8(3Q26.31) MUTATED`
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3529 
       16.57        37.25        14.53        32.45        38.99         0.00 
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3939 TCGA-AA-3966 
        6.05        85.05        10.06        32.05        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01T 
       21.99         7.96        13.94        27.02        32.02        33.04 
TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6600 TCGA-CA-6716 
       21.37         5.79        16.44        33.01        12.10        12.20 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5540 
       13.02        15.02         5.03        11.08        11.01        56.09 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6931 
       20.19         1.32        43.27        17.85         4.80        12.00 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6297 TCGA-G4-6317 
       11.38         7.50       131.51        35.97        82.39        36.00 
TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 
       42.77        30.28        11.90        34.49        14.50        32.02 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-4001 TCGA-AG-4005 
       20.05        12.03        19.99        37.02        36.03        14.04 
TCGA-AG-A02G TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 
       38.96         6.05         4.01         5.29        19.96        20.91 
TCGA-EI-6882 TCGA-EI-7002 TCGA-G5-6233 
        8.61        11.97        18.28 

$`DEL PEAK  8(3Q26.31) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       42.28        44.91        35.11        45.60        13.94        37.05 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.02        34.65        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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.18        24.16        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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         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-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        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        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        15.52        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        10.88         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        16.31         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69         3.06         2.14         3.25         3.29         0.07 
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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04         8.02        27.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        32.02        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         2.96        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-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.26        19.59        55.92        20.42        17.75        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 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        9.44        11.64         1.51        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-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        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 
       16.24        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      133.18        28.21         8.35        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        85.48        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        61.91        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        17.85        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        31.30        21.90        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
        2.01        50.04         6.05         0.99        15.95        13.94 
TCGA-AG-3612 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-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        19.99        28.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       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-6509 
       51.48        32.61         0.49         2.40        20.55        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-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-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        12.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  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 
                         16.57                          20.20 
[1] "0.0 - 131.5 (16.6)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    45  17
  DEL PEAK  8(3Q26.31) WILD-TYPE 401 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     45   17
  DEL PEAK  8(3Q26.31) WILD-TYPE  401  145
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON                            45                            401
  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        1        22         0
  DEL PEAK  8(3Q26.31) WILD-TYPE      99        1       35       151        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3Q26.31) MUTATED           1         3          0          6
  DEL PEAK  8(3Q26.31) WILD-TYPE         2        23         18         77
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3Q26.31) MUTATED            9       12         4         0
  DEL PEAK  8(3Q26.31) WILD-TYPE         45       51        22         2
D35V4, 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                              1                             35
  STAGE IIA                            22                            151
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             3                             23
  STAGE IIIA                            0                             18
  STAGE IIIB                            6                             77
  STAGE IIIC                            9                             45
  STAGE IV                             12                             51
  STAGE IVA                             4                             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
  DEL PEAK  8(3Q26.31) MUTATED     0   6  48   9
  DEL PEAK  8(3Q26.31) WILD-TYPE  20 100 369  58
D35V5, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  T1                            0                             20
  T2                            6                            100
  T3                           48                            369
  T4                            9                             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  8(3Q26.31) MUTATED    31  14  18
  DEL PEAK  8(3Q26.31) WILD-TYPE 314 136  97
D35V6, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  N0                           31                            314
  N1                           14                            136
  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"
D35V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    42  15
  DEL PEAK  8(3Q26.31) WILD-TYPE 408  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     42   15
  DEL PEAK  8(3Q26.31) WILD-TYPE  408   73
   clus
vv  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  0                           42                            408
  1                           15                             73
[1] 2 2
[1] FALSE
D35V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    26  37
  DEL PEAK  8(3Q26.31) WILD-TYPE 261 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     26   37
  DEL PEAK  8(3Q26.31) WILD-TYPE  261  288
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  FEMALE                           26                            261
  MALE                             37                            288
[1] 2 2
[1] FALSE
D35V9, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    52   1
  DEL PEAK  8(3Q26.31) WILD-TYPE 394  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     52    1
  DEL PEAK  8(3Q26.31) WILD-TYPE  394   27
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  NO                            52                            394
  YES                            1                             27
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                     42
  DEL PEAK  8(3Q26.31) WILD-TYPE                  340
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                               3
  DEL PEAK  8(3Q26.31) WILD-TYPE                            57
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                      11
  DEL PEAK  8(3Q26.31) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                                5
  DEL PEAK  8(3Q26.31) WILD-TYPE                              8
D35V10, multiclass
                                clus
vv                               DEL PEAK  8(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                     42
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      340
  COLON MUCINOUS ADENOCARCINOMA                              57
  RECTAL ADENOCARCINOMA                                     135
  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   5   2
  DEL PEAK  8(3Q26.31) WILD-TYPE 394   5  32  27
D35V11, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  R0                           48                            394
  R1                            0                              5
  R2                            5                             32
  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"
D35V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3Q26.31) MUTATED                                  0     2
  DEL PEAK  8(3Q26.31) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q26.31) MUTATED                           8    31
  DEL PEAK  8(3Q26.31) WILD-TYPE                        56   261
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      31
                                  clus
vv                                 DEL PEAK  8(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED     0  40
  DEL PEAK  8(3Q26.31) WILD-TYPE   5 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED      0   40
  DEL PEAK  8(3Q26.31) WILD-TYPE    5  308
                        clus
vv                       DEL PEAK  8(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           40
                        clus
vv                       DEL PEAK  8(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            308
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  9(4P16.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P16.2) MUTATED   150  42
  DEL PEAK  9(4P16.2) WILD-TYPE 322  79
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          192                           401 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                           42                            79 
$`DEL PEAK  9(4P16.2) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        43.76        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4105 
       35.11        13.94        16.57        37.05        37.02        14.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       32.45        30.44        29.16        25.18        21.76        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-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 
       38.99        37.05        34.03        12.99        21.01        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 
       19.99         6.05        54.02         2.01        50.04        15.02 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       36.00        85.05        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-3860 
       10.06        33.07        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 
       53.00        17.03        24.03        29.98         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 
        2.01        20.98         2.01        21.99        50.99        26.01 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       34.03        42.02        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 
       26.01         2.96        39.98         2.01        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D 
       22.42         0.20        14.50         0.95        33.01        17.85 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 
        5.65         5.13        65.00        12.10        29.56         3.19 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        2.14         3.29        49.08         8.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.98        15.02        17.03         2.96        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       20.19        17.75        14.30         9.04         4.80        11.38 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 
       12.59         7.50         6.12        14.04        26.47         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 
       16.24        33.67        47.41         8.35        23.51        63.62 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 
       61.91        91.79        46.75        18.18        10.98        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
       42.77        29.46        21.90        11.90        24.13        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       43.04        34.49        37.74        14.50        15.39        10.39 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       65.98        36.03        46.03        34.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
        6.05        13.94        20.98        29.98        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.03        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-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X 
       25.97        23.01        12.00        70.03        38.96        41.00 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 
        0.69        10.19         6.05        33.17         4.73         5.03 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        27.95        10.98        19.99       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       32.61         2.40        15.85        16.34        16.41        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
        8.45        31.30        28.57         0.39         0.69        26.43 

$`DEL PEAK  9(4P16.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       15.62        12.66         9.53        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       24.33        42.28        45.60        37.25        34.65        36.53 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       19.66        16.24        24.92         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        6.97        14.01         0.92        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        37.05        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        14.93         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       36.03        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        24.00        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        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        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77       100.01         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07        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         9.99        21.14        82.95         1.91       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 
       12.26        19.59        55.92        20.42        18.25         1.32 
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-D5-6923 
       16.14        15.58         1.48         3.68         4.41        12.43 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
        6.18        47.87        34.42        41.42        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        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-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        12.79        17.85        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       31.30        30.28        70.03        39.48        13.55        19.10 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       10.39        16.83        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07        20.05        24.00 
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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       19.99        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 
       19.99        17.95        36.95        13.02        14.01         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
       17.03         3.98        46.03        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       15.95        36.03         9.07         1.02        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 
       10.98        51.98        49.97         1.94        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
       38.56         1.45         0.72        26.43         1.81         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02         8.98        13.97         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.29        41.36        57.24        24.13        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-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-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
        9.96        49.51        32.19         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        12.46        18.28        55.76        47.08 

  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                       129.27                        148.01 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                       21.385                        19.590 
[1] "0.2 - 129.3 (21.4)" "0.0 - 148.0 (19.6)"
[1] "hr=" "1.2"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   135  62
  DEL PEAK  9(4P16.2) WILD-TYPE 311 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    135   62
  DEL PEAK  9(4P16.2) WILD-TYPE  311  100
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  COLON                          135                           311
  RECTUM                          62                           100
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(4P16.2) MUTATED        28        0        7        49         2
  DEL PEAK  9(4P16.2) WILD-TYPE      76        1       29       124         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(4P16.2) MUTATED           0         6          8         25
  DEL PEAK  9(4P16.2) WILD-TYPE         3        20         10         58
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(4P16.2) MUTATED           24       34        12         0
  DEL PEAK  9(4P16.2) WILD-TYPE         30       29        14         2
D36V4, multiclass
            clus
vv           DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  STAGE I                             28                            76
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           49                           124
  STAGE IIB                            2                             8
  STAGE IIC                            0                             3
  STAGE III                            6                            20
  STAGE IIIA                           8                            10
  STAGE IIIB                          25                            58
  STAGE IIIC                          24                            30
  STAGE IV                            34                            29
  STAGE IVA                           12                            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(4P16.2) MUTATED     6  33 135  25
  DEL PEAK  9(4P16.2) WILD-TYPE  14  73 282  42
D36V5, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  T1                           6                            14
  T2                          33                            73
  T3                         135                           282
  T4                          25                            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  9(4P16.2) MUTATED    91  57  51
  DEL PEAK  9(4P16.2) WILD-TYPE 254  93  64
D36V6, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  N0                          91                           254
  N1                          57                            93
  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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   130  43
  DEL PEAK  9(4P16.2) WILD-TYPE 320  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    130   43
  DEL PEAK  9(4P16.2) WILD-TYPE  320   45
   clus
vv  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  0                         130                           320
  1                          43                            45
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED    84 115
  DEL PEAK  9(4P16.2) WILD-TYPE 203 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED     84  115
  DEL PEAK  9(4P16.2) WILD-TYPE  203  210
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  FEMALE                          84                           203
  MALE                           115                           210
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   142  16
  DEL PEAK  9(4P16.2) WILD-TYPE 304  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    142   16
  DEL PEAK  9(4P16.2) WILD-TYPE  304   12
     clus
vv    DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  NO                          142                           304
  YES                          16                            12
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                    124
  DEL PEAK  9(4P16.2) WILD-TYPE                  258
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                              11
  DEL PEAK  9(4P16.2) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                      57
  DEL PEAK  9(4P16.2) WILD-TYPE                    89
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                                4
  DEL PEAK  9(4P16.2) WILD-TYPE                              9
D36V10, multiclass
                                clus
vv                               DEL PEAK  9(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                   124
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   57
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  9(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     258
  COLON MUCINOUS ADENOCARCINOMA                             49
  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(4P16.2) MUTATED   145   0  16   6
  DEL PEAK  9(4P16.2) WILD-TYPE 297   5  21  23
D36V11, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  R0                         145                           297
  R1                           0                             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"
D36V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4P16.2) MUTATED                                  1     2
  DEL PEAK  9(4P16.2) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4P16.2) MUTATED                          22    91
  DEL PEAK  9(4P16.2) WILD-TYPE                        42   201
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  9(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK  9(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED     3 105
  DEL PEAK  9(4P16.2) WILD-TYPE   2 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED      3  105
  DEL PEAK  9(4P16.2) WILD-TYPE    2  243
                        clus
vv                       DEL PEAK  9(4P16.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       DEL PEAK  9(4P16.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           243
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED   168  46
  DEL PEAK 10(4Q22.1) WILD-TYPE 304  75
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          214                           379 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           46                            75 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 
       35.11        13.94        16.57        37.05        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 
       32.45        30.44        29.19        29.16        24.16        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-3510 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3529 
        7.04        63.98         6.97        38.99        37.05         0.00 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 
       34.03        29.00        33.99        21.01        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3715 
        6.05         2.01        50.04        37.05        36.00        19.04 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       10.06        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3952 
       33.07         0.99        31.07        17.03         2.01         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 
       20.98        34.03         2.01        21.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A01C 
       24.00        27.02        34.03        42.02        17.03        15.02 
TCGA-AA-A01F TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 
       32.02        26.01         2.96        39.98        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D 
       22.42         0.20        14.50        16.31         0.95        17.85 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
       18.84         5.13       106.75        65.00        12.10        29.56 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-4750 
        2.14         3.29        14.30       148.01        49.08         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       13.02        29.06        22.03         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
        2.96        29.03        13.02        15.02        11.01        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.08        11.01        45.40        56.09        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        1.32        43.27        15.12        14.30         9.04         4.80 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       12.00        11.38        24.43        12.59         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 
        6.12        14.04        35.97        31.96        16.24        33.67 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 
       47.41        28.21         8.35        82.39        23.51        63.62 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       61.91        91.79        46.75        18.18        10.98         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       16.80        42.77        29.46        21.90        30.28        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 
       37.74        14.50        15.39        65.98        36.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       34.03         6.05        13.94        19.99        20.98        29.98 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 
       32.98        19.04         1.02        17.95         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       13.94         6.02        25.97        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       64.01         1.94        41.00        38.56         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
        6.05        33.17         4.73        11.01         5.03        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE 
       27.95        10.98        19.99         4.01       126.44       129.27 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
        2.40        20.91        17.00        15.85        16.34        16.41 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69        18.28        26.43 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       24.33        42.28        45.60        37.25        37.02        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       16.24        24.92         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       35.01        58.03         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 
       24.03        36.03         8.05        19.07        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       26.01        12.99         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05        26.99        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 
        0.00        36.03        32.05        31.07        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01        24.00        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        14.99        21.99        34.98         1.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72        27.42        10.88        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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07        12.20        12.76        10.06 
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         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       32.02        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       21.99        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       10.06        12.03        12.26        19.59        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 
       15.58         1.48         3.68         4.41        12.43         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.64         1.51        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        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-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
       13.25         0.53        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-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.79        17.85        32.98         8.42        31.30 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       70.03        39.48        10.39        16.83        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
       36.95        17.03        13.02        35.01        14.01        32.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        3.98        46.03        20.98        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        9.07         1.02        31.00        10.98        51.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.96        61.97        38.04         1.45         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.97         9.37        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 
       21.01        15.02         8.98        13.97         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
        0.49        20.55        19.96        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 
        8.61        11.51        10.78        13.64        17.46         9.96 
TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
       49.51         0.53         1.12         0.76        12.46        55.76 
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 
                        19.99                         20.02 
[1] "0.0 - 148.0 (20.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   147  70
  DEL PEAK 10(4Q22.1) WILD-TYPE 299  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    147   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                          147                           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         2
  DEL PEAK 10(4Q22.1) WILD-TYPE      78        1       25       114         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4Q22.1) MUTATED           1         6          7         37
  DEL PEAK 10(4Q22.1) WILD-TYPE         2        20         11         46
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4Q22.1) MUTATED           28       27        11         1
  DEL PEAK 10(4Q22.1) WILD-TYPE         26       36        15         1
D37V4, 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                            25
  STAGE IIA                           59                           114
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           7                            11
  STAGE IIIB                          37                            46
  STAGE IIIC                          28                            26
  STAGE IV                            27                            36
  STAGE IVA                           11                            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 10(4Q22.1) MUTATED     6  29 158  28
  DEL PEAK 10(4Q22.1) WILD-TYPE  14  77 259  39
D37V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                           6                            14
  T2                          29                            77
  T3                         158                           259
  T4                          28                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 10(4Q22.1) MUTATED   102  65  54
  DEL PEAK 10(4Q22.1) WILD-TYPE 243  85  61
D37V6, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                         102                           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"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   153  38
  DEL PEAK 10(4Q22.1) WILD-TYPE 297  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    153   38
  DEL PEAK 10(4Q22.1) WILD-TYPE  297   50
   clus
vv  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  0                         153                           297
  1                          38                            50
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    93 128
  DEL PEAK 10(4Q22.1) WILD-TYPE 194 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     93  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                          93                           194
  MALE                           128                           197
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   160  15
  DEL PEAK 10(4Q22.1) WILD-TYPE 286  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    160   15
  DEL PEAK 10(4Q22.1) WILD-TYPE  286   13
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                          160                           286
  YES                          15                            13
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                    136
  DEL PEAK 10(4Q22.1) WILD-TYPE                  246
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              11
  DEL PEAK 10(4Q22.1) WILD-TYPE                            49
                               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
D37V10, multiclass
                                clus
vv                               DEL PEAK 10(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   136
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     246
  COLON MUCINOUS ADENOCARCINOMA                             49
  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   163   2  12   8
  DEL PEAK 10(4Q22.1) WILD-TYPE 279   3  25  21
D37V11, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                         163                           279
  R1                           2                             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"
D37V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4Q22.1) MUTATED                                  0     3
  DEL PEAK 10(4Q22.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q22.1) MUTATED                          28   109
  DEL PEAK 10(4Q22.1) WILD-TYPE                        36   183
D37V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     3 128
  DEL PEAK 10(4Q22.1) WILD-TYPE   2 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      3  128
  DEL PEAK 10(4Q22.1) WILD-TYPE    2  220
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         128
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 11(4Q35.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.1) MUTATED   176  46
  DEL PEAK 11(4Q35.1) WILD-TYPE 296  75
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          222                           371 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           46                            75 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 
        4.80         1.61        39.45        43.76        43.43        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6649 
       32.45        29.19        29.16        22.52        24.13        24.16 
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-3511 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
        9.63         5.03         6.97        38.99        37.05        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        26.01        14.01        33.99        21.01        13.02 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 
       19.99        78.08         6.05        54.02         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 
       37.05        36.00        85.05        10.06        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03        10.06        33.07        36.03         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.07        17.03         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 
       21.99        16.08        50.99        26.01        24.00         7.96 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       34.03        38.04        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         0.20        14.50        16.31         0.95 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 
       17.85       109.28         5.65         5.13        65.00        12.10 
TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 
       29.56        12.69         2.14        10.06        14.30        49.08 
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         2.96        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         1.32        43.27        17.85 
TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
        1.48         9.04         4.80        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 
       44.32       131.51         6.12        14.04        26.47        31.96 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
        1.55        16.24        33.67        47.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       23.51        63.62        61.91        91.79        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98         9.93        12.79        16.80        42.77        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       21.90        30.28        11.90        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       15.39        65.98        36.03        46.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 
        6.05        13.94        19.99        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-A00H 
       28.04        36.03        14.04         3.98        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 
       23.01        12.00        70.03        64.01        41.00        38.56 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 
        0.69        10.19         6.05        33.17         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA 
        5.03        15.02        27.95        10.98        19.99       126.44 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
      129.27        24.13         2.40        17.00        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.41        11.97         9.96        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
       32.19         0.66         0.53        12.46        18.28        26.43 

$`DEL PEAK 11(4Q35.1) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       24.33        42.28        44.91        37.02        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 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-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       58.03        63.98         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       29.00        12.99         0.99        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       23.01        20.98        19.99        13.94        61.02         6.97 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
       14.93         0.00         0.00         0.00        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       13.05        34.06        25.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98         1.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       18.84        75.95        58.39         1.41        32.94       106.75 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        88.21        49.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.61         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07        12.20        12.76        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         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 
       25.02        26.04        27.02        32.02        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-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       19.59        55.92        20.42        18.25        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         3.68         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        49.91        12.59       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 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-F4-6805 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-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        28.21        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F7 
       74.79        79.69        19.33        19.33        15.65        17.85 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 
       32.98         8.42        31.30        70.03        39.48        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3591 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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99        37.02         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       32.02         1.02        17.03        46.03        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
       38.04         1.45         0.72        26.43         1.81         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        9.37        12.39        78.12         7.17        21.01        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        8.98        13.97         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       19.96        20.91        18.28        17.69        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         8.45        49.51 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.76        55.76        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 
                        20.98                         19.59 
[1] "0.2 - 140.4 (21.0)" "0.0 - 148.0 (19.6)"
[1] "hr=" "1.1"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   157  69
  DEL PEAK 11(4Q35.1) WILD-TYPE 289  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    157   69
  DEL PEAK 11(4Q35.1) WILD-TYPE  289   93
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON                          157                           289
  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        9        63         1
  DEL PEAK 11(4Q35.1) WILD-TYPE      73        1       27       110         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q35.1) MUTATED           1         9          7         35
  DEL PEAK 11(4Q35.1) WILD-TYPE         2        17         11         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q35.1) MUTATED           29       30        10         1
  DEL PEAK 11(4Q35.1) WILD-TYPE         25       33        16         1
D38V4, 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                             9                            27
  STAGE IIA                           63                           110
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            9                            17
  STAGE IIIA                           7                            11
  STAGE IIIB                          35                            48
  STAGE IIIC                          29                            25
  STAGE IV                            30                            33
  STAGE IVA                           10                            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 11(4Q35.1) MUTATED     7  34 163  26
  DEL PEAK 11(4Q35.1) WILD-TYPE  13  72 254  41
D38V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                           7                            13
  T2                          34                            72
  T3                         163                           254
  T4                          26                            41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 11(4Q35.1) MUTATED   109  64  57
  DEL PEAK 11(4Q35.1) WILD-TYPE 236  86  58
D38V6, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                         109                           236
  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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   162  41
  DEL PEAK 11(4Q35.1) WILD-TYPE 288  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    162   41
  DEL PEAK 11(4Q35.1) WILD-TYPE  288   47
   clus
vv  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  0                         162                           288
  1                          41                            47
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   107 123
  DEL PEAK 11(4Q35.1) WILD-TYPE 180 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    107  123
  DEL PEAK 11(4Q35.1) WILD-TYPE  180  202
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                         107                           180
  MALE                           123                           202
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   166  16
  DEL PEAK 11(4Q35.1) WILD-TYPE 280  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    166   16
  DEL PEAK 11(4Q35.1) WILD-TYPE  280   12
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                          166                           280
  YES                          16                            12
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                    140
  DEL PEAK 11(4Q35.1) WILD-TYPE                  242
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              16
  DEL PEAK 11(4Q35.1) WILD-TYPE                            44
                               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
D38V10, multiclass
                                clus
vv                               DEL PEAK 11(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                   140
  COLON MUCINOUS ADENOCARCINOMA                           16
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     242
  COLON MUCINOUS ADENOCARCINOMA                             44
  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   166   1  15   9
  DEL PEAK 11(4Q35.1) WILD-TYPE 276   4  22  20
D38V11, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         166                           276
  R1                           1                             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"
D38V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q35.1) MUTATED                                  1     4
  DEL PEAK 11(4Q35.1) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q35.1) MUTATED                          30   109
  DEL PEAK 11(4Q35.1) WILD-TYPE                        34   183
D38V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 30
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 11(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   34
  WHITE                                                      183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED     3 133
  DEL PEAK 11(4Q35.1) WILD-TYPE   2 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      3  133
  DEL PEAK 11(4Q35.1) WILD-TYPE    2  215
                        clus
vv                       DEL PEAK 11(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         133
                        clus
vv                       DEL PEAK 11(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           215
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED   117  37
  DEL PEAK 12(5Q12.1) WILD-TYPE 355  84
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          154                           439 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           37                            84 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61        39.45        43.76        43.76        43.43        42.90 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        16.57        37.02        34.65        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       30.44        29.19        27.09        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3502 
       21.76        24.69        23.87         9.63         5.03        35.01 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 
       26.01        12.99        13.02        24.00        19.99        50.04 
TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 
       47.01        37.05        19.00        85.05        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 
       37.02        33.07         0.99        31.07        31.07        24.03 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
        2.01         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-A54L TCGA-AY-A71X TCGA-AZ-4614 
       27.42         0.20        16.31        17.26        19.33         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 
       65.00        62.79        29.56         5.23         1.61         3.29 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       14.30        49.08        25.02         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         2.96        29.03        13.02 
TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       17.75        17.85         1.48         4.41        12.43         9.04 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 
       44.32       131.51         6.12         8.61         1.55        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T 
        8.35        82.39        63.62        36.00        91.79        18.18 
TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       10.98        12.79        42.77         8.42        21.90        30.28 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
       24.13        17.23        43.04        37.74        10.39        15.39 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3591 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 
       10.39        86.63        34.03        13.94        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 
       37.02        32.98        19.04        19.99        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A00Y 
       48.03        28.04        36.03        17.03         3.98        23.01 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 
       70.03        64.01         1.94        38.96        41.00        10.19 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       33.17         7.17         5.03        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98         4.01       126.44        57.24       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       20.55        16.41        13.64        11.97         8.45        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6641 
       28.57        32.19        18.28        26.43 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2677 
       15.62         4.80        12.66         9.53        46.65        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        45.60        37.05        37.25 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        22.52        24.13         8.38 
TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       20.61        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05         1.02        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       14.93         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       36.03        32.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01        24.00        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        38.04         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         5.79        10.88        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-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.85        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41        32.94         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       12.69         3.06         2.14         3.25         0.07        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-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32         9.99        21.14        82.95         1.91 
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-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-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        12.26 
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-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       16.14        15.58         3.68        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38         7.50       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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18        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        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       55.04        85.48        39.42        35.93        61.91        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        79.69        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H 
       17.85        16.80        29.46        32.98        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       70.03        39.48        13.55        19.10        34.49        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 
        7.99         0.99         0.99         0.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       36.95        13.02        35.01        14.01        32.02        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       12.00        31.00        10.98        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.05         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
       78.12        21.01        11.01        15.02         8.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 
        5.95         5.03         5.29        41.36        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       10.78        17.46         9.96        31.30         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        12.46        55.76 
TCGA-G5-6572 
       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 
                       22.715                        19.330 
[1] "0.2 - 131.5 (22.7)" "0.0 - 148.0 (19.3)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   105  53
  DEL PEAK 12(5Q12.1) WILD-TYPE 341 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    105   53
  DEL PEAK 12(5Q12.1) WILD-TYPE  341  109
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON                          105                           341
  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        7        35         1
  DEL PEAK 12(5Q12.1) WILD-TYPE      79        1       29       138         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(5Q12.1) MUTATED           1         5          8         19
  DEL PEAK 12(5Q12.1) WILD-TYPE         2        21         10         64
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(5Q12.1) MUTATED           19       20        13         1
  DEL PEAK 12(5Q12.1) WILD-TYPE         35       43        13         1
D39V4, 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                             7                            29
  STAGE IIA                           35                           138
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           8                            10
  STAGE IIIB                          19                            64
  STAGE IIIC                          19                            35
  STAGE IV                            20                            43
  STAGE IVA                           13                            13
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(5Q12.1) MUTATED     5  29 107  17
  DEL PEAK 12(5Q12.1) WILD-TYPE  15  77 310  50
D39V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  T1                           5                            15
  T2                          29                            77
  T3                         107                           310
  T4                          17                            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 12(5Q12.1) MUTATED    76  44  38
  DEL PEAK 12(5Q12.1) WILD-TYPE 269 106  77
D39V6, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  N0                          76                           269
  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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   103  32
  DEL PEAK 12(5Q12.1) WILD-TYPE 347  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    103   32
  DEL PEAK 12(5Q12.1) WILD-TYPE  347   56
   clus
vv  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  0                         103                           347
  1                          32                            56
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    71  87
  DEL PEAK 12(5Q12.1) WILD-TYPE 216 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     71   87
  DEL PEAK 12(5Q12.1) WILD-TYPE  216  238
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  FEMALE                          71                           216
  MALE                            87                           238
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   121   8
  DEL PEAK 12(5Q12.1) WILD-TYPE 325  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    121    8
  DEL PEAK 12(5Q12.1) WILD-TYPE  325   20
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                          121                           325
  YES                           8                            20
[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                            52
                               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
D39V10, 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                             52
  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   2   9   5
  DEL PEAK 12(5Q12.1) WILD-TYPE 333   3  28  24
D39V11, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                         109                           333
  R1                           2                             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"
D39V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(5Q12.1) MUTATED                                  1     2
  DEL PEAK 12(5Q12.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q12.1) MUTATED                          21    80
  DEL PEAK 12(5Q12.1) WILD-TYPE                        43   212
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                     80
                                  clus
vv                                 DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      212
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     3  96
  DEL PEAK 12(5Q12.1) WILD-TYPE   2 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      3   96
  DEL PEAK 12(5Q12.1) WILD-TYPE    2  252
                        clus
vv                       DEL PEAK 12(5Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       DEL PEAK 12(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           252
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 13(5Q21.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q21.2) MUTATED   135  45
  DEL PEAK 13(5Q21.2) WILD-TYPE 337  76
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          180                           413 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                           45                            76 
$`DEL PEAK 13(5Q21.2) MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 
        1.61        39.45        43.76        43.76        13.94        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 
       37.02        36.53        14.53        30.44        29.19        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 
       24.13        25.08        25.18        24.16        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3496 TCGA-AA-3522 
       20.28        56.25         9.63         5.03         1.02        37.05 
TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 
       19.07        26.01        12.99        13.02        24.00        19.99 
TCGA-AA-3655 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 
       61.02        50.04        47.01        15.02        11.01        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       85.05        10.06        36.95        37.02        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 
        0.99        31.07        31.07        17.03        24.03        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3994 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
        2.01        21.99        27.02        34.03        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H 
       17.03        15.02        10.98        33.04         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
        5.03        41.00        22.42        27.42         0.20         0.46 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 
       16.31        21.44        19.33         5.65       106.75        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 
       62.79        29.56         5.23         1.61        12.69         3.29 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
       14.30        49.08        25.02        26.04         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 
       29.06        22.03         5.03        15.02         2.96        29.03 
TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 
       13.02        11.08        19.59        20.42        15.12        17.85 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
        4.41        12.43         9.04         4.80        11.38        92.75 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      140.38        44.32         7.76         6.12        14.04        26.47 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 
      117.07        98.24         8.61        31.96         1.55        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T 
        8.35        82.39        63.62        36.00        91.79        18.18 
TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       10.98        12.79        42.77         8.42        21.90        30.28 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
       24.13        17.23        43.04        37.74        10.39        15.39 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3611 
       10.39        86.63        65.98        32.02        34.03        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99        20.98         7.99        29.98        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       19.04        19.99        17.03         1.02        48.03        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01W 
       36.03        17.03         3.98         6.02        23.01        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CI-6620 
       64.01         1.94        38.96        41.00        10.19        33.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        5.03        13.97        15.02        27.95        10.98         4.01 
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 TCGA-G5-6233 
       16.41        13.64         9.96        28.57        12.46        18.28 

$`DEL PEAK 13(5Q21.2) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
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-A6-5661 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-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 
       19.66        16.24        24.92        61.84         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1.02        37.05        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07         0.00        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       29.00         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        13.94        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.05         5.98        37.05        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 
        0.00         0.00        36.03        32.05        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        38.04         4.01         0.99 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98         1.02        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37        15.52        56.55         0.79         0.72         5.79 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       10.88        16.44         0.92        14.50        27.09         0.95 
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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       75.95        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         2.14         3.25         0.07        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-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32         9.99        21.14        82.95         1.91 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 
      124.27        23.05        20.02        37.02        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-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        45.40        12.26        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       20.19        17.75        18.25         1.32        43.27         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         1.48         3.68 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59         7.50       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
      119.93        35.97        60.79        95.18        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        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       55.04        85.48        39.42        35.93        61.91        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        79.69        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H 
       17.85        16.80        29.46        32.98        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       70.03        39.48        13.55        19.10        34.49        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       16.83        20.02        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        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-3727 TCGA-AG-3742 TCGA-AG-3878 
        0.99        15.95        19.99         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-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-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        31.00        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         1.81         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
        8.98        19.99         5.95         5.03         5.29        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
      129.27        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       20.91        17.00        15.85        17.69        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        17.46        11.97         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        55.76        47.08        26.43 

  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 
                       20.485                        19.990 
[1] "0.2 - 140.4 (20.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   131  55
  DEL PEAK 13(5Q21.2) WILD-TYPE 315 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    131   55
  DEL PEAK 13(5Q21.2) WILD-TYPE  315  107
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON                          131                           315
  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        8        41         1
  DEL PEAK 13(5Q21.2) WILD-TYPE      78        1       28       132         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q21.2) MUTATED           1         6          9         29
  DEL PEAK 13(5Q21.2) WILD-TYPE         2        20          9         54
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q21.2) MUTATED           22       24        14         1
  DEL PEAK 13(5Q21.2) WILD-TYPE         32       39        12         1
D40V4, 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                             8                            28
  STAGE IIA                           41                           132
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           9                             9
  STAGE IIIB                          29                            54
  STAGE IIIC                          22                            32
  STAGE IV                            24                            39
  STAGE IVA                           14                            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 13(5Q21.2) MUTATED     4  32 129  21
  DEL PEAK 13(5Q21.2) WILD-TYPE  16  74 288  46
D40V5, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            74
  T3                         129                           288
  T4                          21                            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 13(5Q21.2) MUTATED    85  56  45
  DEL PEAK 13(5Q21.2) WILD-TYPE 260  94  70
D40V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  N0                          85                           260
  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"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   125  37
  DEL PEAK 13(5Q21.2) WILD-TYPE 325  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    125   37
  DEL PEAK 13(5Q21.2) WILD-TYPE  325   51
   clus
vv  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  0                         125                           325
  1                          37                            51
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED    86 100
  DEL PEAK 13(5Q21.2) WILD-TYPE 201 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED     86  100
  DEL PEAK 13(5Q21.2) WILD-TYPE  201  225
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  FEMALE                          86                           201
  MALE                           100                           225
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   139   9
  DEL PEAK 13(5Q21.2) WILD-TYPE 307  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    139    9
  DEL PEAK 13(5Q21.2) WILD-TYPE  307   19
     clus
vv    DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  NO                          139                           307
  YES                           9                            19
[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                            46
                               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
D40V10, 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                             46
  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   2  13   7
  DEL PEAK 13(5Q21.2) WILD-TYPE 316   3  24  22
D40V11, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  R0                         126                           316
  R1                           2                             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"
D40V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q21.2) MUTATED                                  1     3
  DEL PEAK 13(5Q21.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q21.2) MUTATED                          21    91
  DEL PEAK 13(5Q21.2) WILD-TYPE                        43   201
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK 13(5Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED     3 108
  DEL PEAK 13(5Q21.2) WILD-TYPE   2 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED      3  108
  DEL PEAK 13(5Q21.2) WILD-TYPE    2  240
                        clus
vv                       DEL PEAK 13(5Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       DEL PEAK 13(5Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 14(5Q22.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q22.2) MUTATED   134  46
  DEL PEAK 14(5Q22.2) WILD-TYPE 338  75
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          180                           413 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           46                            75 
$`DEL PEAK 14(5Q22.2) MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 
        1.61        39.45        43.76        43.76        13.94        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 
       37.02        36.53        14.53        30.44        29.19        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 
       24.13        25.08        25.18        24.16        21.76        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 
        9.63         5.03         1.02         1.02        37.05        19.07 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3655 
       26.01        12.99        13.02        24.00        19.99        61.02 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       50.04        47.01        15.02        19.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       10.06        36.95        37.02        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       31.07        17.03        24.03        24.00         2.01        21.99 
TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D 
       19.07        34.03        27.02        42.02        15.02        10.98 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 
       33.04         2.96         2.01         5.03        41.00        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A71X 
       27.42        10.88         0.20        16.31        21.44        19.33 
TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 
        5.65       106.75        65.00        62.79         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 
        5.23         1.61         2.14         3.29        14.30        49.08 
TCGA-CK-6751 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
      124.27        25.02        26.04         8.02        13.02        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 
        5.03        15.02         2.96        29.03        13.02        11.08 
TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       19.59        15.12        17.85         4.41        12.43         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 
        4.80        11.38        92.75       140.38        44.32         7.76 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12        26.47        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 
       31.96         1.55        33.67         8.35        82.39        63.62 
TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV 
       36.00        91.79        18.18        10.98        12.79        42.77 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
        8.42        21.90        30.28        24.13        17.23        43.04 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        15.39        10.39        86.63        65.98 
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       32.02        34.03        13.94        19.99        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 
       37.02        32.98        19.04        19.99        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A00C 
       48.03        28.04        36.03        17.03         3.98         6.02 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       23.01        12.00        70.03        64.01         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 
       41.00         1.81        10.19        33.17         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA 
       13.97        15.02        27.95        10.98         4.01       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       41.36        57.24        51.48        20.55        19.96        18.28 
TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
       16.34        16.41         9.96        28.57        12.46        18.28 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
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-A6-5661 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-3506 TCGA-AA-3510 
        7.04         3.02        37.05        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 
       24.03        36.03         8.05        19.07         0.00        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
        0.92        47.05        11.01         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       17.03         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        1.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98        39.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72         5.79        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        33.01        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        18.84       109.28        75.95        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-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         3.19        12.69         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.20        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         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 
       82.95         1.91        23.05        20.02        37.02        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58         1.48         3.68        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        49.91        13.32        12.59         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        11.11        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        16.24        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18        28.21        23.51        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-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        61.91        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        46.75        74.79        79.69        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33         9.93        15.65        17.85        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 
       32.98        31.30        11.90        70.03        39.48        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56N 
       19.10        34.49        14.50        16.83        20.02        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         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-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 
        7.99         0.99         0.99         0.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       36.95        13.02        35.01        14.01        32.02        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H 
       14.04         1.02        46.03        20.98        13.94        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       10.98        51.98        49.97        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 
        1.45         0.69         0.72        26.43         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.73        12.39        78.12        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.02         8.98        19.99         5.95         5.03         5.29 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
      129.27        24.13        32.61         0.49         2.40        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       17.00        15.85        17.69        16.31         8.61        11.51 
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-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        55.76        47.08        26.43 

  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 
                        19.99                         19.99 
[1] "0.2 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D41V2, continuous
D41V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   129  59
  DEL PEAK 14(5Q22.2) WILD-TYPE 317 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    129   59
  DEL PEAK 14(5Q22.2) WILD-TYPE  317  103
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON                          129                           317
  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        9        45         0
  DEL PEAK 14(5Q22.2) WILD-TYPE      77        1       27       128        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q22.2) MUTATED           1         6          8         28
  DEL PEAK 14(5Q22.2) WILD-TYPE         2        20         10         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q22.2) MUTATED           21       24        13         1
  DEL PEAK 14(5Q22.2) WILD-TYPE         33       39        13         1
D41V4, 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                             9                            27
  STAGE IIA                           45                           128
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           8                            10
  STAGE IIIB                          28                            55
  STAGE IIIC                          21                            33
  STAGE IV                            24                            39
  STAGE IVA                           13                            13
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(5Q22.2) MUTATED     4  32 132  20
  DEL PEAK 14(5Q22.2) WILD-TYPE  16  74 285  47
D41V5, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            74
  T3                         132                           285
  T4                          20                            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 14(5Q22.2) MUTATED    92  53  43
  DEL PEAK 14(5Q22.2) WILD-TYPE 253  97  72
D41V6, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          92                           253
  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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   125  36
  DEL PEAK 14(5Q22.2) WILD-TYPE 325  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    125   36
  DEL PEAK 14(5Q22.2) WILD-TYPE  325   52
   clus
vv  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  0                         125                           325
  1                          36                            52
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    83 105
  DEL PEAK 14(5Q22.2) WILD-TYPE 204 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     83  105
  DEL PEAK 14(5Q22.2) WILD-TYPE  204  220
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          83                           204
  MALE                           105                           220
[1] 2 2
[1] FALSE
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   135  10
  DEL PEAK 14(5Q22.2) WILD-TYPE 311  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    135   10
  DEL PEAK 14(5Q22.2) WILD-TYPE  311   18
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                          135                           311
  YES                          10                            18
[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                            47
                               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
D41V10, 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                             47
  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   2  15   8
  DEL PEAK 14(5Q22.2) WILD-TYPE 319   3  22  21
D41V11, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                         123                           319
  R1                           2                             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"
D41V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q22.2) MUTATED                                  1     3
  DEL PEAK 14(5Q22.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q22.2) MUTATED                          20    93
  DEL PEAK 14(5Q22.2) WILD-TYPE                        44   199
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK 14(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED     3 108
  DEL PEAK 14(5Q22.2) WILD-TYPE   2 240
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      3  108
  DEL PEAK 14(5Q22.2) WILD-TYPE    2  240
                        clus
vv                       DEL PEAK 14(5Q22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       DEL PEAK 14(5Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           240
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    58  18
  DEL PEAK 15(6P25.3) WILD-TYPE 414 103
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           76                           517 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           18                           103 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       43.76        16.57        37.02        25.18        24.16        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
       36.00        19.04        38.99        36.95        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 
       29.98        18.05        12.99        24.00         2.01        13.94 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O 
       30.02        18.05        27.02        38.07        26.01         0.92 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
        0.72         5.79        10.88        16.44         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
       12.69         3.06         2.14        29.06        22.98        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       11.01        45.40        20.19        17.75        17.85         1.48 
TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6317 TCGA-T9-A92H 
       13.32        26.47       117.07        33.67        36.00        11.90 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3584 
       17.23        13.55        19.10        34.49        14.50        24.00 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3611 TCGA-AG-4001 
       34.03        34.03        34.03        50.04        13.94        36.03 
TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-BM-6198 TCGA-DC-4745 TCGA-DC-6682 
        3.98        13.94        37.02        10.19        21.01         4.01 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
        5.29        24.13        15.85        11.51 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
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-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 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-A6-6650 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-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       20.98        19.99        19.99        78.08         6.05        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        37.02        14.93         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-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 
        0.99        31.07        17.03        24.03        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       27.02        38.04        19.00        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13       106.75        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 
      100.01        29.56         5.23        11.74         1.61         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07        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-5912 
       17.56       148.01        85.45        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.03        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 
        2.96        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-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        10.06        12.03        12.26        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         1.32        43.27        15.12 
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         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        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 
        4.80         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        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-F4-6704 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        16.24        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      133.18        28.21         8.35        82.39        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       63.62        39.42        35.93        61.91        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        17.85        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        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 
       70.03        24.13        39.48        43.04        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        15.39        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 
       36.03        20.05         1.02        46.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 
        6.05         0.99        15.95        19.99        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       46.03        20.98         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72        26.43         1.81         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.73        12.39        78.12         7.17        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        19.99         5.95         5.03       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         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         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        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.72                          0.00 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       117.07                        148.01 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       18.545                        20.020 
[1] "0.7 - 117.1 (18.5)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    55  21
  DEL PEAK 15(6P25.3) WILD-TYPE 391 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     55   21
  DEL PEAK 15(6P25.3) WILD-TYPE  391  141
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  COLON                           55                           391
  RECTUM                          21                           141
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(6P25.3) MUTATED         9        0        7        29         1
  DEL PEAK 15(6P25.3) WILD-TYPE      95        1       29       144         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED           1         4          1          6
  DEL PEAK 15(6P25.3) WILD-TYPE         2        22         17         77
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(6P25.3) MUTATED            7        7         5         0
  DEL PEAK 15(6P25.3) WILD-TYPE         47       56        21         2
D42V4, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              9                            95
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           29                           144
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            4                            22
  STAGE IIIA                           1                            17
  STAGE IIIB                           6                            77
  STAGE IIIC                           7                            47
  STAGE IV                             7                            56
  STAGE IVA                            5                            21
  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(6P25.3) MUTATED     2   9  58  10
  DEL PEAK 15(6P25.3) WILD-TYPE  18  97 359  57
D42V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           2                            18
  T2                           9                            97
  T3                          58                           359
  T4                          10                            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 15(6P25.3) MUTATED    48  15  16
  DEL PEAK 15(6P25.3) WILD-TYPE 297 135  99
D42V6, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          48                           297
  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"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    56  11
  DEL PEAK 15(6P25.3) WILD-TYPE 394  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     56   11
  DEL PEAK 15(6P25.3) WILD-TYPE  394   77
   clus
vv  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  0                          56                           394
  1                          11                            77
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    29  50
  DEL PEAK 15(6P25.3) WILD-TYPE 258 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     29   50
  DEL PEAK 15(6P25.3) WILD-TYPE  258  275
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          29                           258
  MALE                            50                           275
[1] 2 2
[1] FALSE
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    57   7
  DEL PEAK 15(6P25.3) WILD-TYPE 389  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     57    7
  DEL PEAK 15(6P25.3) WILD-TYPE  389   21
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                           57                           389
  YES                           7                            21
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                     49
  DEL PEAK 15(6P25.3) WILD-TYPE                  333
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                               5
  DEL PEAK 15(6P25.3) WILD-TYPE                            55
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                      18
  DEL PEAK 15(6P25.3) WILD-TYPE                   128
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                                3
  DEL PEAK 15(6P25.3) WILD-TYPE                             10
D42V10, multiclass
                                clus
vv                               DEL PEAK 15(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                    49
  COLON MUCINOUS ADENOCARCINOMA                            5
  RECTAL ADENOCARCINOMA                                   18
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 15(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     333
  COLON MUCINOUS ADENOCARCINOMA                             55
  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 15(6P25.3) MUTATED    56   0   3   6
  DEL PEAK 15(6P25.3) WILD-TYPE 386   5  34  23
D42V11, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          56                           386
  R1                           0                             5
  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"
D42V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(6P25.3) MUTATED                                  0     4
  DEL PEAK 15(6P25.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED                           2    38
  DEL PEAK 15(6P25.3) WILD-TYPE                        62   254
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 15(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     38
                                  clus
vv                                 DEL PEAK 15(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   62
  WHITE                                                      254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     0  41
  DEL PEAK 15(6P25.3) WILD-TYPE   5 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      0   41
  DEL PEAK 15(6P25.3) WILD-TYPE    5  307
                        clus
vv                       DEL PEAK 15(6P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          41
                        clus
vv                       DEL PEAK 15(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           307
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 16(6Q26) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED    63  23
  DEL PEAK 16(6Q26) WILD-TYPE 409  98
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         86                         507 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         23                          98 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6649 
       43.76        42.28        45.60        32.45        22.52        24.16 
TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       20.28         5.03        13.02        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3837 
       11.01        37.05        36.00        85.05        19.04        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        36.03        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        2.01        18.05        17.03        10.98        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         5.79        16.44         0.46        16.31 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       18.84         5.13        49.41         3.19        12.69         3.06 
TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
        2.14        11.01        13.05        11.08        11.01        45.40 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-DM-A1HA 
       20.19        17.75        15.12         1.48        13.32       131.51 
TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2690 TCGA-AF-2691 
        1.55        33.67        82.39         9.93        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AG-3575 TCGA-AG-3578 
       13.55        19.10        34.49        37.74        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 
       24.00        46.03        34.03        34.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 
       19.99        13.94        14.04         1.02        13.94        37.02 
TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 
       38.56         0.72         9.37         4.01         5.29         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 16(6Q26) WILD-TYPE`
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-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        24.33        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        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-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-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       19.00         5.03        26.99        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       24.03        27.02        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       37.02        39.06        51.98        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37        15.52        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88         0.20         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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.61         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       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         2.96        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        12.26 
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         1.32 
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         3.68         4.41        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         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       49.91        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
       47.87        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
       47.41        35.31       133.18        28.21         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       85.48        63.62        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33        15.65        12.79        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 
       30.28        11.90        70.03        24.13        39.48        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03         8.02         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-3612 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-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-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03        17.03         3.98        46.03        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-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-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       33.17         6.97         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        27.95        10.98        19.99         5.95         5.03 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
       12.46        55.76        47.08 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                       0.46                        0.00 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     131.51                      148.01 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                      17.90                       20.55 
[1] "0.5 - 131.5 (17.9)" "0.0 - 148.0 (20.6)"
[1] "hr=" "1.6"
D43V2, continuous
D43V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    61  28
  DEL PEAK 16(6Q26) WILD-TYPE 385 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     61   28
  DEL PEAK 16(6Q26) WILD-TYPE  385  134
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  COLON                         61                         385
  RECTUM                        28                         134
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6Q26) MUTATED        13        0        8        20         1
  DEL PEAK 16(6Q26) WILD-TYPE      91        1       28       153         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q26) MUTATED           1         4          1         10
  DEL PEAK 16(6Q26) WILD-TYPE         2        22         17         73
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6Q26) MUTATED           14       12         4         1
  DEL PEAK 16(6Q26) WILD-TYPE         40       51        22         1
D43V4, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                           13                          91
  STAGE IA                           0                           1
  STAGE II                           8                          28
  STAGE IIA                         20                         153
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          4                          22
  STAGE IIIA                         1                          17
  STAGE IIIB                        10                          73
  STAGE IIIC                        14                          40
  STAGE IV                          12                          51
  STAGE IVA                          4                          22
  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 16(6Q26) MUTATED     5  10  64  12
  DEL PEAK 16(6Q26) WILD-TYPE  15  96 353  55
D43V5, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T1                         5                          15
  T2                        10                          96
  T3                        64                         353
  T4                        12                          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 16(6Q26) MUTATED    42  18  30
  DEL PEAK 16(6Q26) WILD-TYPE 303 132  85
D43V6, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                        42                         303
  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"
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    59  18
  DEL PEAK 16(6Q26) WILD-TYPE 391  70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     59   18
  DEL PEAK 16(6Q26) WILD-TYPE  391   70
   clus
vv  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  0                        59                         391
  1                        18                          70
[1] 2 2
[1] FALSE
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    37  54
  DEL PEAK 16(6Q26) WILD-TYPE 250 271
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     37   54
  DEL PEAK 16(6Q26) WILD-TYPE  250  271
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        37                         250
  MALE                          54                         271
[1] 2 2
[1] FALSE
D43V9, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    63   8
  DEL PEAK 16(6Q26) WILD-TYPE 383  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     63    8
  DEL PEAK 16(6Q26) WILD-TYPE  383   20
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                         63                         383
  YES                         8                          20
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                     52
  DEL PEAK 16(6Q26) WILD-TYPE                  330
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                               8
  DEL PEAK 16(6Q26) WILD-TYPE                            52
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                      22
  DEL PEAK 16(6Q26) WILD-TYPE                   124
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                6
  DEL PEAK 16(6Q26) WILD-TYPE                              7
D43V10, multiclass
                                clus
vv                               DEL PEAK 16(6Q26) MUTATED
  COLON ADENOCARCINOMA                                  52
  COLON MUCINOUS ADENOCARCINOMA                          8
  RECTAL ADENOCARCINOMA                                 22
  RECTAL MUCINOUS ADENOCARCINOMA                         6
                                clus
vv                               DEL PEAK 16(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                   330
  COLON MUCINOUS ADENOCARCINOMA                           52
  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 16(6Q26) MUTATED    61   1   8   7
  DEL PEAK 16(6Q26) WILD-TYPE 381   4  29  22
D43V11, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                        61                         381
  R1                         1                           4
  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"
D43V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6Q26) MUTATED                                  1     4
  DEL PEAK 16(6Q26) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q26) MUTATED                           5    39
  DEL PEAK 16(6Q26) WILD-TYPE                        59   253
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 16(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   39
                                  clus
vv                                 DEL PEAK 16(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 59
  WHITE                                                    253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     0  45
  DEL PEAK 16(6Q26) WILD-TYPE   5 303
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      0   45
  DEL PEAK 16(6Q26) WILD-TYPE    5  303
                        clus
vv                       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                        45                         303
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 17(7Q31.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q31.1) MUTATED    13   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 459 118
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           577 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            3                           118 
$`DEL PEAK 17(7Q31.1) MUTATED`
TCGA-5M-AAT4 TCGA-A6-3807 TCGA-AA-A00L TCGA-AA-A01R TCGA-AD-6548 TCGA-AU-3779 
        1.61        34.65        38.04        35.01        21.37        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         4.01 

$`DEL PEAK 17(7Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        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-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
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-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-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-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        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-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.20        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       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-5348 
       25.02        26.04         8.02        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02        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         2.96        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-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        12.26        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         1.32        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 
        1.48         3.68         4.41        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64         4.80         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        17.85        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        30.28        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        34.49        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        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-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
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-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         1.61                          0.00 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        38.04                        148.01 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                       18.195                        19.990 
[1] "1.6 - 38.0 (18.2)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    13   4
  DEL PEAK 17(7Q31.1) WILD-TYPE 433 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     13    4
  DEL PEAK 17(7Q31.1) WILD-TYPE  433  158
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON                           13                           433
  RECTUM                           4                           158
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(7Q31.1) MUTATED         3        0        0         7         0
  DEL PEAK 17(7Q31.1) WILD-TYPE     101        1       36       166        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 17(7Q31.1) WILD-TYPE         3        25         17         82
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(7Q31.1) MUTATED            2        1         1         0
  DEL PEAK 17(7Q31.1) WILD-TYPE         52       62        25         2
D44V4, multiclass
            clus
vv           DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  STAGE I                              3                           101
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                            7                           166
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            1                            25
  STAGE IIIA                           1                            17
  STAGE IIIB                           1                            82
  STAGE IIIC                           2                            52
  STAGE IV                             1                            62
  STAGE IVA                            1                            25
  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 17(7Q31.1) MUTATED     0   4  13   0
  DEL PEAK 17(7Q31.1) WILD-TYPE  20 102 404  67
D44V5, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           102
  T3                          13                           404
  T4                           0                            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 17(7Q31.1) MUTATED    11   3   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 334 147 112
D44V6, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                          11                           334
  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"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    15   2
  DEL PEAK 17(7Q31.1) WILD-TYPE 435  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     15    2
  DEL PEAK 17(7Q31.1) WILD-TYPE  435   86
   clus
vv  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  0                          15                           435
  1                           2                            86
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     9   8
  DEL PEAK 17(7Q31.1) WILD-TYPE 278 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      9    8
  DEL PEAK 17(7Q31.1) WILD-TYPE  278  317
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           9                           278
  MALE                             8                           317
[1] 2 2
[1] FALSE
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    11   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 435  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     11    3
  DEL PEAK 17(7Q31.1) WILD-TYPE  435   25
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  NO                           11                           435
  YES                           3                            25
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                     12
  DEL PEAK 17(7Q31.1) WILD-TYPE                  370
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                               1
  DEL PEAK 17(7Q31.1) WILD-TYPE                            59
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                       3
  DEL PEAK 17(7Q31.1) WILD-TYPE                   143
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                                1
  DEL PEAK 17(7Q31.1) WILD-TYPE                             12
D44V10, multiclass
                                clus
vv                               DEL PEAK 17(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    12
  COLON MUCINOUS ADENOCARCINOMA                            1
  RECTAL ADENOCARCINOMA                                    3
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     370
  COLON MUCINOUS ADENOCARCINOMA                             59
  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 17(7Q31.1) MUTATED    16   0   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 426   5  37  29
D44V11, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  R0                          16                           426
  R1                           0                             5
  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"
D44V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q31.1) MUTATED                                  0     0
  DEL PEAK 17(7Q31.1) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(7Q31.1) MUTATED                           1    10
  DEL PEAK 17(7Q31.1) WILD-TYPE                        63   282
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 17(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     10
                                  clus
vv                                 DEL PEAK 17(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   63
  WHITE                                                      282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     2   9
  DEL PEAK 17(7Q31.1) WILD-TYPE   3 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      2    9
  DEL PEAK 17(7Q31.1) WILD-TYPE    3  339
                        clus
vv                       DEL PEAK 17(7Q31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK 17(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           339
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED   220  62
  DEL PEAK 18(8P23.2) WILD-TYPE 252  59
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          282                           311 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           62                            59 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61         9.53        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       24.33        42.28        44.91        35.11        45.60        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       34.65        36.53        32.91        31.63        29.19        23.61 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        24.13        25.08        25.18        20.61 
TCGA-A6-6652 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-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 
        5.03         1.02        37.05         1.02        38.99        24.03 
TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        0.00        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       19.99        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       85.05        37.02        33.07        36.03         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        29.98         2.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
        2.01        34.03        16.08        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A017 
       27.02         7.96        19.00        34.03        17.03         1.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       12.00        31.00         1.02        33.04        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 
       39.98         5.03        41.00        40.96        15.52         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
       22.42         0.20        16.31        33.01        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 
      109.28         5.65       106.75        65.00        62.79        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 
       29.56         5.23        11.74         3.19         1.61         3.29 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 
        0.07        14.30        15.62        49.08        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 
        2.96        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        12.26        56.09        55.92        17.75         1.32 
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         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04         4.80        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
      130.65        49.91        13.32       140.38       131.51         6.12 
TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 
       26.47        35.97        60.79       117.07        31.96        35.74 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
        1.55        34.42         0.53         8.35        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        39.42        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       26.43        35.80        91.79        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2689 
       15.65        16.80         8.42        21.90        30.28        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        19.10        34.49        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       10.39        15.39        20.02        10.39        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-3611 TCGA-AG-3612 
       34.03         2.01         6.05         0.99        13.94        19.99 
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-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
        1.02        17.03        35.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        25.97        23.01        15.95         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 
        1.94        38.96        41.00         1.45         0.72        10.19 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        12.39        78.12        21.01        11.01         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        27.95        10.98         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 
        5.29       126.44        41.36        57.24       129.27         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        2.40        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        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69         0.76        12.46        18.28        26.43 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 
       15.62        12.66        39.45        46.65        42.90        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 
       37.05        37.25        37.02        14.53        32.45        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        22.06        32.71        22.52         8.38 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.16        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       24.92         7.04         3.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 
        6.97         1.02        13.02         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3554 
       36.03         8.05        19.07        19.07        29.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
        0.92        50.04        47.05        11.01         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        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-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
        0.00        17.03        10.06         0.00         0.00        32.05 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       53.00        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       26.01        24.00        20.98         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       13.05        25.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C 
       42.02         0.99        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02O 
       35.01        26.01        39.06        51.98         2.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72        27.42        10.88        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-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.26        19.33        75.95        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        5.13        22.36        88.21        49.41         6.77       100.01 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
       12.69         3.06         2.14         3.25        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
       10.06        17.56       148.01        85.45        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 
       20.02        37.02        25.02        26.04         8.02        29.06 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 
       11.08        11.01        12.03        45.40        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        18.25        17.85         4.80        17.13        16.14 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
        3.68        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26       119.70        92.75        12.59         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18         8.61        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       47.87        41.42        16.24        33.67        13.25        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        28.21        82.39        67.30        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        63.62        22.09        26.04        13.78 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       26.17        46.75        74.79        79.69        18.18        19.33 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       12.79        17.85        42.77        29.46        32.98        31.30 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K 
       11.90        70.03        24.13        14.50        16.83        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       11.84        36.03        12.00         8.02         7.07        20.05 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 
       50.04        12.03        15.95        19.99        20.98        37.02 
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-3898 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 
       48.03        46.03        13.94         6.02        37.02        36.03 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04        38.56         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 
        1.81         6.05        33.17         6.97         9.37         7.17 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG 
       15.02         8.98        19.99         5.95        24.13        51.48 
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-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 
       17.69        16.31        16.41         8.61        17.46        49.51 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6572 
       32.19         0.53         1.12        55.76        47.08 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                            0                             0 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       20.005                        19.990 
[1] "0.0 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   188  98
  DEL PEAK 18(8P23.2) WILD-TYPE 258  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    188   98
  DEL PEAK 18(8P23.2) WILD-TYPE  258   64
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  COLON                          188                           258
  RECTUM                          98                            64
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(8P23.2) MUTATED        40        0       12        64         3
  DEL PEAK 18(8P23.2) WILD-TYPE      64        1       24       109         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(8P23.2) MUTATED           2        13         10         45
  DEL PEAK 18(8P23.2) WILD-TYPE         1        13          8         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(8P23.2) MUTATED           33       46        14         1
  DEL PEAK 18(8P23.2) WILD-TYPE         21       17        12         1
D45V4, multiclass
            clus
vv           DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                             40                            64
  STAGE IA                             0                             1
  STAGE II                            12                            24
  STAGE IIA                           64                           109
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           13                            13
  STAGE IIIA                          10                             8
  STAGE IIIB                          45                            38
  STAGE IIIC                          33                            21
  STAGE IV                            46                            17
  STAGE IVA                           14                            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 18(8P23.2) MUTATED     4  47 203  34
  DEL PEAK 18(8P23.2) WILD-TYPE  16  59 214  33
D45V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T1                           4                            16
  T2                          47                            59
  T3                         203                           214
  T4                          34                            33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 18(8P23.2) MUTATED   133  81  73
  DEL PEAK 18(8P23.2) WILD-TYPE 212  69  42
D45V6, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                         133                           212
  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"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   197  59
  DEL PEAK 18(8P23.2) WILD-TYPE 253  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    197   59
  DEL PEAK 18(8P23.2) WILD-TYPE  253   29
   clus
vv  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  0                         197                           253
  1                          59                            29
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   122 166
  DEL PEAK 18(8P23.2) WILD-TYPE 165 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    122  166
  DEL PEAK 18(8P23.2) WILD-TYPE  165  159
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                         122                           165
  MALE                           166                           159
[1] 2 2
[1] FALSE
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   203  14
  DEL PEAK 18(8P23.2) WILD-TYPE 243  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    203   14
  DEL PEAK 18(8P23.2) WILD-TYPE  243   14
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                          203                           243
  YES                          14                            14
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                    170
  DEL PEAK 18(8P23.2) WILD-TYPE                  212
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                              15
  DEL PEAK 18(8P23.2) WILD-TYPE                            45
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                      89
  DEL PEAK 18(8P23.2) WILD-TYPE                    57
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                7
  DEL PEAK 18(8P23.2) WILD-TYPE                              6
D45V10, multiclass
                                clus
vv                               DEL PEAK 18(8P23.2) MUTATED
  COLON ADENOCARCINOMA                                   170
  COLON MUCINOUS ADENOCARCINOMA                           15
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 18(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     212
  COLON MUCINOUS ADENOCARCINOMA                             45
  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 18(8P23.2) MUTATED   199   2  26   9
  DEL PEAK 18(8P23.2) WILD-TYPE 243   3  11  20
D45V11, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                         199                           243
  R1                           2                             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"
D45V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P23.2) MUTATED                                  1     4
  DEL PEAK 18(8P23.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED                          32   136
  DEL PEAK 18(8P23.2) WILD-TYPE                        32   156
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     4 162
  DEL PEAK 18(8P23.2) WILD-TYPE   1 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      4  162
  DEL PEAK 18(8P23.2) WILD-TYPE    1  186
                        clus
vv                       DEL PEAK 18(8P23.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         162
                        clus
vv                       DEL PEAK 18(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           186
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 19(8P22) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(8P22) MUTATED   224  70
  DEL PEAK 19(8P22) WILD-TYPE 248  51
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        294                         299 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                         70                          51 
$`DEL PEAK 19(8P22) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61         9.53        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       24.33        42.28        44.91        35.11        45.60        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       23.61        29.16        27.09        24.13        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        24.69        23.87        20.28        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 
        9.63         5.03         1.02        37.05         1.02        38.99 
TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       24.03         0.00        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       19.99        19.99        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       19.00        36.00        85.05        37.02        10.06        33.07 
TCGA-AA-3854 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       36.03        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       29.98         2.01         2.01        34.03        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
       38.04        17.03         1.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
       33.04        37.02         2.96         5.03        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 
       15.52         5.79        22.42         0.20         0.46        16.31 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       33.01        17.85        19.33        18.84       109.28         5.65 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 
      106.75        22.36        65.00        62.79        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 
        5.23        11.74         3.19         1.61         3.29        14.30 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
      148.01        15.62        49.08        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         2.96 
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-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       10.06        12.26        19.59        56.09        55.92        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        1.32        43.27        15.12        12.49        15.58         1.48 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
        4.41        12.43         9.04         4.80        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51         6.12        26.47        35.97        60.79       117.07 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        11.11        35.74         1.55        34.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       13.25         0.53         8.35        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       26.04        35.80        91.79        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        30.28 
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        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       37.74        10.39        15.39        20.02        10.39        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-3611 
       34.03        34.03         2.01         6.05         0.99        13.94 
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-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 
        1.02        17.95        17.03        35.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        3.98        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
       51.98         1.94        38.96        41.00         1.45         0.72 
TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       10.19         4.73        12.39        78.12        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        5.03        13.97        15.02        27.95        10.98         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         5.29       126.44        41.36        57.24       129.27 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 
        0.49         2.40        15.85        16.34        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        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.39         0.69         0.76        12.46        18.28        26.43 

$`DEL PEAK 19(8P22) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 
       15.62        12.66        39.45        46.65        42.90        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 
       37.05        37.25        37.02        14.53        32.45        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 
       22.09        22.06        32.71        22.52         8.38        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 
        8.05        19.07        19.07        29.00         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 
       29.95        20.98        13.94        61.02         6.97         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       50.04        47.05         5.03        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3875 
        0.00         0.00        32.05         0.99        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
       20.98         2.01        21.99        50.99        13.05        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        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-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       21.99        34.98        15.02        10.98        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       38.07         1.02        35.01        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         2.01         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88        16.44         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        21.44        17.82        17.26        75.95        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-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
      100.01        12.69         3.06         2.14         3.25         0.07 
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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32         9.99        21.14        82.95         1.91       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       29.06        15.02        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       29.03        16.04        14.99        12.99        14.04        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       11.08        11.01        12.03        45.40        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 
       18.25        17.85         4.80        17.13        16.14         3.68 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
      119.70        92.75        12.59         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M 
      139.17        14.04        81.37       119.93        98.24        95.18 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         6.18        47.87        41.42        16.24        33.67 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18        28.21        82.39        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 
       53.62        55.04        85.48        63.62        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC 
       26.17        74.79        79.69        18.18        19.33        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-T9-A92H 
       17.85        42.77        29.46        32.98        31.30        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N 
       70.03        24.13        14.50        16.83        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 
       36.03        12.00         8.02         7.07        20.05        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3731 
       12.03        15.95        19.99        19.99        20.98        37.02 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 
        0.99        19.99        36.95        13.02        14.01        48.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A025 
       46.03        20.98        13.94         6.02        36.03        49.97 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       61.97        38.04        38.56         0.69        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 
        6.05        33.17         6.97         9.37         7.17        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        8.98        19.99         5.95        24.13        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 
       16.31        16.41         8.61        17.46        49.51        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.53         1.12        55.76        47.08 

  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                          0                           0 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                     148.01                      139.17 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                      20.15                       19.99 
[1] "0.0 - 148.0 (20.1)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.5"
D46V2, continuous
D46V3, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   201  98
  DEL PEAK 19(8P22) WILD-TYPE 245  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    201   98
  DEL PEAK 19(8P22) WILD-TYPE  245   64
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  COLON                        201                         245
  RECTUM                        98                          64
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P22) MUTATED        40        0       13        66         3
  DEL PEAK 19(8P22) WILD-TYPE      64        1       23       107         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P22) MUTATED           2        14         11         47
  DEL PEAK 19(8P22) WILD-TYPE         1        12          7         36
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P22) MUTATED           36       46        17         1
  DEL PEAK 19(8P22) WILD-TYPE         18       17         9         1
D46V4, multiclass
            clus
vv           DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  STAGE I                           40                          64
  STAGE IA                           0                           1
  STAGE II                          13                          23
  STAGE IIA                         66                         107
  STAGE IIB                          3                           7
  STAGE IIC                          2                           1
  STAGE III                         14                          12
  STAGE IIIA                        11                           7
  STAGE IIIB                        47                          36
  STAGE IIIC                        36                          18
  STAGE IV                          46                          17
  STAGE IVA                         17                           9
  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(8P22) MUTATED     4  47 213  37
  DEL PEAK 19(8P22) WILD-TYPE  16  59 204  30
D46V5, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  T1                         4                          16
  T2                        47                          59
  T3                       213                         204
  T4                        37                          30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 19(8P22) MUTATED   137  84  79
  DEL PEAK 19(8P22) WILD-TYPE 208  66  36
D46V6, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  N0                       137                         208
  N1                        84                          66
  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"
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   206  62
  DEL PEAK 19(8P22) WILD-TYPE 244  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    206   62
  DEL PEAK 19(8P22) WILD-TYPE  244   26
   clus
vv  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  0                       206                         244
  1                        62                          26
[1] 2 2
[1] FALSE
D46V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   132 169
  DEL PEAK 19(8P22) WILD-TYPE 155 156
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    132  169
  DEL PEAK 19(8P22) WILD-TYPE  155  156
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  FEMALE                       132                         155
  MALE                         169                         156
[1] 2 2
[1] FALSE
D46V9, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   215  15
  DEL PEAK 19(8P22) WILD-TYPE 231  13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    215   15
  DEL PEAK 19(8P22) WILD-TYPE  231   13
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  NO                        215                         231
  YES                        15                          13
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                    182
  DEL PEAK 19(8P22) WILD-TYPE                  200
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                              16
  DEL PEAK 19(8P22) WILD-TYPE                            44
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                      89
  DEL PEAK 19(8P22) WILD-TYPE                    57
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                                7
  DEL PEAK 19(8P22) WILD-TYPE                              6
D46V10, multiclass
                                clus
vv                               DEL PEAK 19(8P22) MUTATED
  COLON ADENOCARCINOMA                                 182
  COLON MUCINOUS ADENOCARCINOMA                         16
  RECTAL ADENOCARCINOMA                                 89
  RECTAL MUCINOUS ADENOCARCINOMA                         7
                                clus
vv                               DEL PEAK 19(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                   200
  COLON MUCINOUS ADENOCARCINOMA                           44
  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(8P22) MUTATED   212   2  26   8
  DEL PEAK 19(8P22) WILD-TYPE 230   3  11  21
D46V11, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  R0                       212                         230
  R1                         2                           3
  R2                        26                          11
  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"
D46V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P22) MUTATED                                  1     3
  DEL PEAK 19(8P22) WILD-TYPE                                0     9
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P22) MUTATED                          33   147
  DEL PEAK 19(8P22) WILD-TYPE                        31   145
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 19(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               33
  WHITE                                                  147
                                  clus
vv                                 DEL PEAK 19(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED     4 173
  DEL PEAK 19(8P22) WILD-TYPE   1 175
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED      4  173
  DEL PEAK 19(8P22) WILD-TYPE    1  175
                        clus
vv                       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  HISPANIC OR LATINO                             4                           1
  NOT HISPANIC OR LATINO                       173                         175
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 20(8Q11.1) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(8Q11.1) MUTATED    35  11
  DEL PEAK 20(8Q11.1) WILD-TYPE 437 110
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           46                           547 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           11                           110 
$`DEL PEAK 20(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 
       24.33        42.28        44.91        16.57        36.53        20.61 
TCGA-A6-6654 TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-3681 
       23.87        38.99        34.03        14.01         2.01         5.98 
TCGA-AA-3842 TCGA-AA-3989 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02F TCGA-AY-A69D 
       37.02         7.96        10.98        31.00        39.98        17.85 
TCGA-AY-A8YK TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6531 
       18.84        37.02        17.03        13.05        56.09        17.75 
TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6625 TCGA-AF-2689 
       49.91       131.51         1.55        23.51        91.79        39.48 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3582 TCGA-AG-3611 TCGA-AG-3728 TCGA-AG-3890 
       13.55        34.49        36.03        13.94        29.98        17.03 
TCGA-AG-3909 TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6156 
       19.99        12.00        38.96        41.00        13.97        15.02 
TCGA-DY-A1DG TCGA-EI-6513 TCGA-F5-6810 TCGA-F5-6813 
       51.48        16.34         0.39         0.69 

$`DEL PEAK 20(8Q11.1) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2680 
       43.76        46.65        43.76        43.43        42.90        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       45.60        13.94        37.05        37.25        37.02        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-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-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98         1.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13       106.75        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 
        1.91       124.27        23.05        20.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00         2.96        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        12.26        19.59        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        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 
        4.80         1.51        12.00        11.38        10.26       119.70 
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-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-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
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        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       35.31       133.18        28.21         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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        17.85        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        30.28 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       11.90        70.03        24.13        17.23        43.04        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-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-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02         5.03         8.98        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        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-F5-6814 
       49.51        31.30        28.57        32.19         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                         0.39                          0.00 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                        22.06                         19.99 
[1] "0.4 - 131.5 (22.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    30  16
  DEL PEAK 20(8Q11.1) WILD-TYPE 416 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     30   16
  DEL PEAK 20(8Q11.1) WILD-TYPE  416  146
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  COLON                           30                           416
  RECTUM                          16                           146
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8Q11.1) MUTATED         4        0        0        13         1
  DEL PEAK 20(8Q11.1) WILD-TYPE     100        1       36       160         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8Q11.1) MUTATED           0         2          2          7
  DEL PEAK 20(8Q11.1) WILD-TYPE         3        24         16         76
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8Q11.1) MUTATED            7        6         4         1
  DEL PEAK 20(8Q11.1) WILD-TYPE         47       57        22         1
D47V4, multiclass
            clus
vv           DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  STAGE I                              4                           100
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                           13                           160
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           2                            16
  STAGE IIIB                           7                            76
  STAGE IIIC                           7                            47
  STAGE IV                             6                            57
  STAGE IVA                            4                            22
  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(8Q11.1) MUTATED     0   7  35   5
  DEL PEAK 20(8Q11.1) WILD-TYPE  20  99 382  62
D47V5, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  T1                           0                            20
  T2                           7                            99
  T3                          35                           382
  T4                           5                            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 20(8Q11.1) MUTATED    19  16  12
  DEL PEAK 20(8Q11.1) WILD-TYPE 326 134 103
D47V6, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  N0                          19                           326
  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"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    32  11
  DEL PEAK 20(8Q11.1) WILD-TYPE 418  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     32   11
  DEL PEAK 20(8Q11.1) WILD-TYPE  418   77
   clus
vv  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  0                          32                           418
  1                          11                            77
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    18  29
  DEL PEAK 20(8Q11.1) WILD-TYPE 269 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     18   29
  DEL PEAK 20(8Q11.1) WILD-TYPE  269  296
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  FEMALE                          18                           269
  MALE                            29                           296
[1] 2 2
[1] FALSE
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    36   1
  DEL PEAK 20(8Q11.1) WILD-TYPE 410  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     36    1
  DEL PEAK 20(8Q11.1) WILD-TYPE  410   27
     clus
vv    DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  NO                           36                           410
  YES                           1                            27
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                     26
  DEL PEAK 20(8Q11.1) WILD-TYPE                  356
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                               4
  DEL PEAK 20(8Q11.1) WILD-TYPE                            56
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                      15
  DEL PEAK 20(8Q11.1) WILD-TYPE                   131
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                                1
  DEL PEAK 20(8Q11.1) WILD-TYPE                             12
D47V10, multiclass
                                clus
vv                               DEL PEAK 20(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                    26
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   15
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 20(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     356
  COLON MUCINOUS ADENOCARCINOMA                             56
  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 20(8Q11.1) MUTATED    38   0   4   0
  DEL PEAK 20(8Q11.1) WILD-TYPE 404   5  33  29
D47V11, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  R0                          38                           404
  R1                           0                             5
  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"
D47V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8Q11.1) MUTATED                                  1     0
  DEL PEAK 20(8Q11.1) WILD-TYPE                                0    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8Q11.1) MUTATED                           6    22
  DEL PEAK 20(8Q11.1) WILD-TYPE                        58   270
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 20(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     22
                                  clus
vv                                 DEL PEAK 20(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   58
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED     0  29
  DEL PEAK 20(8Q11.1) WILD-TYPE   5 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED      0   29
  DEL PEAK 20(8Q11.1) WILD-TYPE    5  319
                        clus
vv                       DEL PEAK 20(8Q11.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       DEL PEAK 20(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           319
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 21(9P24.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(9P24.2) MUTATED    61  19
  DEL PEAK 21(9P24.2) WILD-TYPE 411 102
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           80                           513 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           19                           102 
$`DEL PEAK 21(9P24.2) MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 
       39.45        43.76        43.43        36.53        14.53        29.16 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       24.16        21.76        61.84         6.97        38.99         9.07 
TCGA-AA-3532 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3819 
       29.00        24.00        19.99        37.05        85.05        25.02 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3972 TCGA-AA-A004 
       24.03        12.99        24.00        20.98        50.99        13.94 
TCGA-AA-A01F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-4614 
       32.02        40.96        15.52         0.20        16.31         5.65 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 
        5.23         3.19         1.61         3.29        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-D5-6533 TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF 
       10.06        20.19         1.32        43.27         1.48        38.20 
TCGA-DM-A288 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2687 
       14.04        33.67         8.35        82.39         9.93        24.13 
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-3896 TCGA-AG-4021 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A026 
       19.99         1.02         3.98        15.95        12.00         1.94 
TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 
       38.96        38.56        10.19         6.05         4.73        12.39 
TCGA-DC-4749 TCGA-DC-6160 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       11.01        19.99        57.24        24.13        51.48         0.49 
TCGA-EI-6514 TCGA-F5-6814 
       16.31         0.53 

$`DEL PEAK 21(9P24.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       34.65        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-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 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-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
        0.99         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        88.21        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       29.56        11.74        12.69         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       85.45        70.16        15.62        49.08        51.32         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        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         2.96        29.03 
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-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       12.95        11.08        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 
       56.09        55.92        20.42        17.75        18.25        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-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        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         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        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-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        16.24        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       47.41        35.31       133.18        28.21        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        74.79        79.69        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        15.65        12.79        17.85        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        30.28 
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        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 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-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04         1.02        17.95        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
       51.98        49.97        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72        26.43         1.81        33.17         6.97 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
        9.37        78.12         7.17        21.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
        8.98        13.97        15.02        27.95        10.98         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE 
        4.01         5.03         5.29       126.44        41.36       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         1.12         0.76        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                        85.05                        148.01 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                        16.31                         20.12 
[1] "0.2 - 85.0 (16.3)"  "0.0 - 148.0 (20.1)"
[1] "hr=" "1.4"
D48V2, continuous
D48V3, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    56  26
  DEL PEAK 21(9P24.2) WILD-TYPE 390 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     56   26
  DEL PEAK 21(9P24.2) WILD-TYPE  390  136
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  COLON                           56                           390
  RECTUM                          26                           136
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(9P24.2) MUTATED        13        0        4        19         1
  DEL PEAK 21(9P24.2) WILD-TYPE      91        1       32       154         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(9P24.2) MUTATED           0         3          3         12
  DEL PEAK 21(9P24.2) WILD-TYPE         3        23         15         71
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(9P24.2) MUTATED            9       12         4         1
  DEL PEAK 21(9P24.2) WILD-TYPE         45       51        22         1
D48V4, multiclass
            clus
vv           DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  STAGE I                             13                            91
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           19                           154
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            3                            23
  STAGE IIIA                           3                            15
  STAGE IIIB                          12                            71
  STAGE IIIC                           9                            45
  STAGE IV                            12                            51
  STAGE IVA                            4                            22
  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(9P24.2) MUTATED     2  16  53  12
  DEL PEAK 21(9P24.2) WILD-TYPE  18  90 364  55
D48V5, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  T1                           2                            18
  T2                          16                            90
  T3                          53                           364
  T4                          12                            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 21(9P24.2) MUTATED    39  24  20
  DEL PEAK 21(9P24.2) WILD-TYPE 306 126  95
D48V6, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  N0                          39                           306
  N1                          24                           126
  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"
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    58  18
  DEL PEAK 21(9P24.2) WILD-TYPE 392  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     58   18
  DEL PEAK 21(9P24.2) WILD-TYPE  392   70
   clus
vv  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  0                          58                           392
  1                          18                            70
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    30  53
  DEL PEAK 21(9P24.2) WILD-TYPE 257 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     30   53
  DEL PEAK 21(9P24.2) WILD-TYPE  257  272
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  FEMALE                          30                           257
  MALE                            53                           272
[1] 2 2
[1] FALSE
D48V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    59   4
  DEL PEAK 21(9P24.2) WILD-TYPE 387  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     59    4
  DEL PEAK 21(9P24.2) WILD-TYPE  387   24
     clus
vv    DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  NO                           59                           387
  YES                           4                            24
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                     53
  DEL PEAK 21(9P24.2) WILD-TYPE                  329
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                               2
  DEL PEAK 21(9P24.2) WILD-TYPE                            58
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                      25
  DEL PEAK 21(9P24.2) WILD-TYPE                   121
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                                1
  DEL PEAK 21(9P24.2) WILD-TYPE                             12
D48V10, multiclass
                                clus
vv                               DEL PEAK 21(9P24.2) MUTATED
  COLON ADENOCARCINOMA                                    53
  COLON MUCINOUS ADENOCARCINOMA                            2
  RECTAL ADENOCARCINOMA                                   25
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 21(9P24.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     329
  COLON MUCINOUS ADENOCARCINOMA                             58
  RECTAL ADENOCARCINOMA                                    121
  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(9P24.2) MUTATED    53   2   7   3
  DEL PEAK 21(9P24.2) WILD-TYPE 389   3  30  26
D48V11, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  R0                          53                           389
  R1                           2                             3
  R2                           7                            30
  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"
D48V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(9P24.2) MUTATED                                  0     2
  DEL PEAK 21(9P24.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(9P24.2) MUTATED                           7    43
  DEL PEAK 21(9P24.2) WILD-TYPE                        57   249
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 21(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     43
                                  clus
vv                                 DEL PEAK 21(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   57
  WHITE                                                      249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED     2  47
  DEL PEAK 21(9P24.2) WILD-TYPE   3 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED      2   47
  DEL PEAK 21(9P24.2) WILD-TYPE    3  301
                        clus
vv                       DEL PEAK 21(9P24.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          47
                        clus
vv                       DEL PEAK 21(9P24.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           301
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 22(10P15.3) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(10P15.3) MUTATED    92  18
  DEL PEAK 22(10P15.3) WILD-TYPE 380 103
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           110                            483 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            18                            103 
$`DEL PEAK 22(10P15.3) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 
       43.76        24.33        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3673 
        1.02         6.97        13.02        19.99        54.02        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       37.05        36.00        85.05        10.06        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       24.03         2.01        50.99        24.00         7.96        34.03 
TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       18.05        42.02        21.99        10.98        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AZ-4323 TCGA-AZ-4614 
       22.42        16.44         0.46        14.50         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
        5.13        65.00        62.79        29.56         3.19         3.29 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 
       12.20        14.30         8.02        29.06        22.03        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-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.75        15.12         1.48         4.41         9.04         4.80 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 
       82.39        65.85        55.04        35.93        61.91        26.04 
TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 
       46.75        12.79        30.28        24.13        13.55        34.49 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 
       10.39        65.98        46.03        34.03        34.03        19.99 
TCGA-AG-3726 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-A008 
        7.99         1.02         1.02        19.99        28.04        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6544 TCGA-CI-6624 
       25.97        23.01        12.00        41.00        38.56         4.73 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       11.01        13.97        15.02        27.95         4.01         5.03 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7004 
       57.24       129.27        17.00        16.31        16.41         8.45 
TCGA-F5-6702 TCGA-G5-6641 
       28.57        26.43 

$`DEL PEAK 22(10P15.3) WILD-TYPE`
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-A6-2671 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-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        24.16        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-3496 
       56.25         5.03         7.04         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
       13.94        61.02        78.08         6.05         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       35.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        0.72         5.79        27.42        10.88         0.20         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-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39        32.94       106.75        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         2.14         3.25         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
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         2.96        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        12.26 
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 
        1.32        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         3.68        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         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
        8.35        23.51        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       85.48        63.62        39.42        36.00        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        74.79        79.69 
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-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        11.90        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
        0.99        15.95        13.94        19.99        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       14.01        48.03        32.02        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
       17.03         3.98        46.03        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05        33.17         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       12.39        78.12         7.17        21.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
        8.98        10.98        19.99         5.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       11.97         9.96        49.51        31.30         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                         22.01                          19.99 
[1] "0.5 - 129.3 (22.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D49V2, continuous
D49V3, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    77  34
  DEL PEAK 22(10P15.3) WILD-TYPE 369 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     77   34
  DEL PEAK 22(10P15.3) WILD-TYPE  369  128
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  COLON                            77                            369
  RECTUM                           34                            128
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(10P15.3) MUTATED        19        0        6        21         0
  DEL PEAK 22(10P15.3) WILD-TYPE      85        1       30       152        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(10P15.3) MUTATED           1         2          6         16
  DEL PEAK 22(10P15.3) WILD-TYPE         2        24         12         67
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(10P15.3) MUTATED           13       17         7         1
  DEL PEAK 22(10P15.3) WILD-TYPE         41       46        19         1
D49V4, multiclass
            clus
vv           DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            21                            152
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            6                             12
  STAGE IIIB                           16                             67
  STAGE IIIC                           13                             41
  STAGE IV                             17                             46
  STAGE IVA                             7                             19
  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(10P15.3) MUTATED     2  23  74  13
  DEL PEAK 22(10P15.3) WILD-TYPE  18  83 343  54
D49V5, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  T1                            2                             18
  T2                           23                             83
  T3                           74                            343
  T4                           13                             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 22(10P15.3) MUTATED    51  32  29
  DEL PEAK 22(10P15.3) WILD-TYPE 294 118  86
D49V6, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  N0                           51                            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"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    77  24
  DEL PEAK 22(10P15.3) WILD-TYPE 373  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     77   24
  DEL PEAK 22(10P15.3) WILD-TYPE  373   64
   clus
vv  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  0                           77                            373
  1                           24                             64
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    51  61
  DEL PEAK 22(10P15.3) WILD-TYPE 236 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     51   61
  DEL PEAK 22(10P15.3) WILD-TYPE  236  264
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  FEMALE                           51                            236
  MALE                             61                            264
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    85   9
  DEL PEAK 22(10P15.3) WILD-TYPE 361  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     85    9
  DEL PEAK 22(10P15.3) WILD-TYPE  361   19
     clus
vv    DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  NO                            85                            361
  YES                            9                             19
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                     69
  DEL PEAK 22(10P15.3) WILD-TYPE                  313
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                               8
  DEL PEAK 22(10P15.3) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                      30
  DEL PEAK 22(10P15.3) WILD-TYPE                   116
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                                4
  DEL PEAK 22(10P15.3) WILD-TYPE                              9
D49V10, multiclass
                                clus
vv                               DEL PEAK 22(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                     69
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    30
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK 22(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      313
  COLON MUCINOUS ADENOCARCINOMA                              52
  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 22(10P15.3) MUTATED    83   0   6   6
  DEL PEAK 22(10P15.3) WILD-TYPE 359   5  31  23
D49V11, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  R0                           83                            359
  R1                            0                              5
  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"
D49V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(10P15.3) MUTATED                                  0     3
  DEL PEAK 22(10P15.3) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(10P15.3) MUTATED                           9    61
  DEL PEAK 22(10P15.3) WILD-TYPE                        55   231
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 22(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      61
                                  clus
vv                                 DEL PEAK 22(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    55
  WHITE                                                       231
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED     1  68
  DEL PEAK 22(10P15.3) WILD-TYPE   4 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED      1   68
  DEL PEAK 22(10P15.3) WILD-TYPE    4  280
                        clus
vv                       DEL PEAK 22(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 22(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            280
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 23(10Q21.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10Q21.1) MUTATED   107  26
  DEL PEAK 23(10Q21.1) WILD-TYPE 365  95
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           133                            460 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            26                             95 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 
        1.61        39.45        43.76        24.33        35.11        45.60 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       34.65        32.45        30.44        32.71        29.16        22.52 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       25.18        20.61        23.87        61.84        56.25         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
        1.02         6.97        38.99        33.99        21.01        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05        50.04        37.05        36.00        85.05 
TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 
       10.06        31.07        17.03        24.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q 
       50.99         7.96        34.03        42.02        10.98         1.02 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 
       26.01        39.98         5.03        41.00         0.79        22.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 
       16.44        14.50        16.31        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         3.29        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         1.48         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 
        4.80        12.00        11.38        35.97       117.07        11.11 
TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 
       55.04        35.93        61.91        26.04        91.79        46.75 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 
       12.79        17.85        30.28        24.13        13.55        34.49 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       16.83        10.39        65.98        32.02        36.03        20.05 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 
       46.03        34.03        34.03        34.03         6.05        29.98 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        36.95         1.02        19.99        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02X TCGA-CI-6622 
       25.97        23.01        12.00         1.94        41.00         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
        4.73        12.39        13.97        27.95         4.01         5.03 
TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6864 
      129.27        17.00        16.31        16.41        28.57        12.46 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       15.62         4.80        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        37.02        36.53        14.53        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-A6-6649 TCGA-A6-6651 
       27.09        24.13         8.38        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       24.92         5.03         7.04         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       12.99         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
        1.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.96         2.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         5.79        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13       106.75        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.61         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        1.91       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        13.02        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00         2.96        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        12.26 
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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
        1.32         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
        3.68         4.41        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
       14.04        26.47        81.37       119.93        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        31.96        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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       53.62        44.68        85.48        63.62        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       26.43        22.09        13.78        35.80        26.17        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
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-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        11.90        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       43.04        19.10        37.74        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99        17.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 
        1.02        17.03         3.98        46.03        20.98        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 
        1.81        10.19         6.05        33.17         9.37        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02        10.98        19.99         5.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                          0.79                           0.00 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                         20.61                          19.99 
[1] "0.8 - 129.3 (20.6)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1"  
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    96  40
  DEL PEAK 23(10Q21.1) WILD-TYPE 350 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     96   40
  DEL PEAK 23(10Q21.1) WILD-TYPE  350  122
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON                            96                            350
  RECTUM                           40                            122
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10Q21.1) MUTATED        20        0        7        32         1
  DEL PEAK 23(10Q21.1) WILD-TYPE      84        1       29       141         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10Q21.1) MUTATED           1         2          6         20
  DEL PEAK 23(10Q21.1) WILD-TYPE         2        24         12         63
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10Q21.1) MUTATED           18       20         6         1
  DEL PEAK 23(10Q21.1) WILD-TYPE         36       43        20         1
D50V4, multiclass
            clus
vv           DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              7                             29
  STAGE IIA                            32                            141
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            6                             12
  STAGE IIIB                           20                             63
  STAGE IIIC                           18                             36
  STAGE IV                             20                             43
  STAGE IVA                             6                             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 23(10Q21.1) MUTATED     3  24  96  14
  DEL PEAK 23(10Q21.1) WILD-TYPE  17  82 321  53
D50V5, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  T1                            3                             17
  T2                           24                             82
  T3                           96                            321
  T4                           14                             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 23(10Q21.1) MUTATED    68  36  33
  DEL PEAK 23(10Q21.1) WILD-TYPE 277 114  82
D50V6, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  N0                           68                            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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    98  26
  DEL PEAK 23(10Q21.1) WILD-TYPE 352  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     98   26
  DEL PEAK 23(10Q21.1) WILD-TYPE  352   62
   clus
vv  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  0                           98                            352
  1                           26                             62
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    62  75
  DEL PEAK 23(10Q21.1) WILD-TYPE 225 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     62   75
  DEL PEAK 23(10Q21.1) WILD-TYPE  225  250
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  FEMALE                           62                            225
  MALE                             75                            250
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    99  14
  DEL PEAK 23(10Q21.1) WILD-TYPE 347  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     99   14
  DEL PEAK 23(10Q21.1) WILD-TYPE  347   14
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                            99                            347
  YES                           14                             14
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                     89
  DEL PEAK 23(10Q21.1) WILD-TYPE                  293
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                               7
  DEL PEAK 23(10Q21.1) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                      34
  DEL PEAK 23(10Q21.1) WILD-TYPE                   112
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                                6
  DEL PEAK 23(10Q21.1) WILD-TYPE                              7
D50V10, multiclass
                                clus
vv                               DEL PEAK 23(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                     89
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      293
  COLON MUCINOUS ADENOCARCINOMA                              53
  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 23(10Q21.1) MUTATED    97   2  12   7
  DEL PEAK 23(10Q21.1) WILD-TYPE 345   3  25  22
D50V11, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           97                            345
  R1                            2                              3
  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"
D50V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10Q21.1) MUTATED                                  0     4
  DEL PEAK 23(10Q21.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10Q21.1) MUTATED                          16    65
  DEL PEAK 23(10Q21.1) WILD-TYPE                        48   227
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 23(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      65
                                  clus
vv                                 DEL PEAK 23(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       227
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED     4  78
  DEL PEAK 23(10Q21.1) WILD-TYPE   1 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED      4   78
  DEL PEAK 23(10Q21.1) WILD-TYPE    1  270
                        clus
vv                       DEL PEAK 23(10Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 23(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED   130  25
  DEL PEAK 24(10Q23.31) WILD-TYPE 342  96
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            155                             438 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             25                              96 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
       39.45        43.76        24.33        42.28        35.11        45.60 
TCGA-A6-2682 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       13.94        32.45        30.44        32.71        29.16        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 
       25.18        24.16        23.87        61.84         9.63         1.02 
TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3556 
        6.97         9.07        19.07        33.99        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 
       19.99         6.05        54.02        50.04        11.01        37.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3860 
       36.00        85.05        36.95        33.07        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F 
       17.03        24.03         2.01        50.99         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W 
       42.02        10.98        33.04        26.01        39.98        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L 
       22.42        16.44         0.46        14.50        16.31        17.26 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 
       17.85         5.65        65.00        62.79        29.56         3.19 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 
       12.69         3.29        12.20        14.30         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 
       22.03        30.08         5.03        15.02        15.02        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       13.02        15.02        13.05        11.08        11.08        10.06 
TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 
       19.59        17.75        18.25        43.27        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 
        1.48         4.41         9.04         4.80       130.65        13.32 
TCGA-DM-A1D9 TCGA-DM-A285 TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 
      140.38         6.12        11.11        16.24        33.67        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC 
       61.91        36.00        26.04        13.78        46.75        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 
       17.85        29.46        30.28        24.13        39.48        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 
       34.49        10.39        65.98        32.02         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3728 
       34.03        34.03        34.03        50.04         6.05        29.98 
TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4021 
       37.02        19.04        36.95         1.02        19.99         3.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
       13.94        25.97        37.02        12.00        10.98        41.00 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-6155 
       26.43        10.19         6.97         4.73        12.39        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
       27.95         4.01         5.03       129.27        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 
        2.40        17.00        16.34        16.31        16.41        11.97 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       28.57         0.66        12.46        47.08        26.43 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.62         4.80        12.66         1.61         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 
       43.76        43.43        42.90        44.91        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        14.53        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-A6-6650 TCGA-A6-6651 
       27.09        24.13         8.38        25.08        20.61        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-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       24.92        56.25         5.03         7.04         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        14.01        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02         5.98        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        37.02        14.93         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-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
        0.99        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98         1.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
        1.02        35.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        0.72         5.79        27.42        10.88         0.20         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X 
       27.09         0.95        33.01        21.44        17.82        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13       106.75        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 
       12.10       100.01         5.23        11.74         1.61         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        2.14         3.25         0.07        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
        9.99        21.14        82.95         1.91       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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.98        32.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
        2.96        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.01        12.95        11.01        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 
       56.09        55.92        20.19        20.42         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
        4.80        17.13        16.14        15.58         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       41.42        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       65.85        53.62        44.68        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       35.93        26.43        22.09        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       74.79        79.69        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 
       31.30        21.90        11.90        70.03        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
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-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 
       17.03        46.03        20.98         6.02        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 
       38.56         1.45         0.69         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       33.17         9.37        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02         5.03         8.98        15.02        10.98        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.95         5.29       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
       32.61        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       17.69         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        31.30         0.39        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.46                            0.00 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         19.990                          20.005 
[1] "0.5 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   107  51
  DEL PEAK 24(10Q23.31) WILD-TYPE 339 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    107   51
  DEL PEAK 24(10Q23.31) WILD-TYPE  339  111
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON                            107                             339
  RECTUM                            51                             111
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q23.31) MUTATED        21        1        6        41         2
  DEL PEAK 24(10Q23.31) WILD-TYPE      83        0       30       132         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q23.31) MUTATED           1         6          9         22
  DEL PEAK 24(10Q23.31) WILD-TYPE         2        20          9         61
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q23.31) MUTATED           17       22         6         2
  DEL PEAK 24(10Q23.31) WILD-TYPE         37       41        20         0
D51V4, multiclass
            clus
vv           DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  STAGE I                               21                              83
  STAGE IA                               1                               0
  STAGE II                               6                              30
  STAGE IIA                             41                             132
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              6                              20
  STAGE IIIA                             9                               9
  STAGE IIIB                            22                              61
  STAGE IIIC                            17                              37
  STAGE IV                              22                              41
  STAGE IVA                              6                              20
  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 24(10Q23.31) MUTATED     3  24 114  16
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  82 303  51
D51V5, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  T1                             3                              17
  T2                            24                              82
  T3                           114                             303
  T4                            16                              51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 24(10Q23.31) MUTATED    77  44  37
  DEL PEAK 24(10Q23.31) WILD-TYPE 268 106  78
D51V6, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  N0                            77                             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"
D51V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   115  29
  DEL PEAK 24(10Q23.31) WILD-TYPE 335  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    115   29
  DEL PEAK 24(10Q23.31) WILD-TYPE  335   59
   clus
vv  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  0                           115                             335
  1                            29                              59
[1] 2 2
[1] FALSE
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    75  84
  DEL PEAK 24(10Q23.31) WILD-TYPE 212 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     75   84
  DEL PEAK 24(10Q23.31) WILD-TYPE  212  241
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                            75                             212
  MALE                              84                             241
[1] 2 2
[1] FALSE
D51V9, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   117  13
  DEL PEAK 24(10Q23.31) WILD-TYPE 329  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    117   13
  DEL PEAK 24(10Q23.31) WILD-TYPE  329   15
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                            117                             329
  YES                            13                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                     96
  DEL PEAK 24(10Q23.31) WILD-TYPE                  286
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                               9
  DEL PEAK 24(10Q23.31) WILD-TYPE                            51
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                      42
  DEL PEAK 24(10Q23.31) WILD-TYPE                   104
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                                7
  DEL PEAK 24(10Q23.31) WILD-TYPE                              6
D51V10, multiclass
                                clus
vv                               DEL PEAK 24(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                      96
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                     42
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       286
  COLON MUCINOUS ADENOCARCINOMA                               51
  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 24(10Q23.31) MUTATED   117   1  12   6
  DEL PEAK 24(10Q23.31) WILD-TYPE 325   4  25  23
D51V11, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                           117                             325
  R1                             1                               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"
D51V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10Q23.31) MUTATED                                  0     4
  DEL PEAK 24(10Q23.31) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED                          17    81
  DEL PEAK 24(10Q23.31) WILD-TYPE                        47   211
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                       81
                                  clus
vv                                 DEL PEAK 24(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     47
  WHITE                                                        211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED     3  96
  DEL PEAK 24(10Q23.31) WILD-TYPE   2 252
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED      3   96
  DEL PEAK 24(10Q23.31) WILD-TYPE    2  252
                        clus
vv                       DEL PEAK 24(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            96
                        clus
vv                       DEL PEAK 24(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             252
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 25(10Q25.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q25.2) MUTATED   118  32
  DEL PEAK 25(10Q25.2) WILD-TYPE 354  89
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           150                            443 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                            32                             89 
$`DEL PEAK 25(10Q25.2) MUTATED`
TCGA-3L-AA1B TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       15.62        39.45        43.76        24.33        42.28        35.11 
TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       45.60        32.45        30.44        32.71        29.16        22.52 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       25.18        20.61        23.87        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 
        5.03         1.02         6.97         9.07        37.05        29.00 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 
       33.99        13.02        19.99         6.05         2.01        50.04 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       11.01        37.05        36.00         5.03        85.05        10.06 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 
        0.99        36.95        33.07         0.99        17.03        24.03 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D 
        2.01        50.99         7.96        34.03        42.02        10.98 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6901 
       33.04        26.01        39.06         0.92        41.00        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 
        0.20        16.44        14.50        16.31        17.85         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 
       65.00        62.79        29.56         3.19         3.29        12.20 
TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
       14.30         1.91        25.02         8.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        5.03        15.02        15.02        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       11.08        11.08        10.06        17.75        43.27        17.85 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 
        1.48         4.41         9.04         4.80        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 
      131.51         6.12        35.97        11.11        16.24        33.67 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 
       55.04        61.91        36.00        26.04        91.79        46.75 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 
       12.79        17.85        30.28        24.13        39.48        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3593 
       34.49        10.39        65.98        32.02        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        6.05        29.98        19.04        36.95        17.03         1.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 
       19.99        36.03         3.98        13.94        25.97        37.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 
       12.00        70.03        10.98        41.00        26.43        10.19 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
        4.73        13.97        27.95        19.99         4.01         5.03 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
      129.27        24.13         2.40        17.00        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       11.97        28.57         0.66        12.46        47.08        26.43 

$`DEL PEAK 25(10Q25.2) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
        4.80        12.66         1.61         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        44.91        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        14.53        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-A6-6649 TCGA-A6-6651 
       27.09        24.13         8.38        25.08        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.92         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3819 
       19.00        26.99        19.04        19.04        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-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-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05        31.07        31.07        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98         1.02 
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        35.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
        0.79         0.72         5.79        27.42        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        19.33        18.84       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41        32.94         5.13       106.75        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        1.61        12.69         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        49.08        51.32         9.99        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-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         2.96        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-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       20.19        20.42        18.25         1.32        15.12         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         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       49.91        12.59         7.50        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-F4-6463 
      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-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        85.48        63.62        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       26.43        22.09        13.78        35.80        26.17        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       79.69        18.18        10.98        19.33        19.33         9.93 
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-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 
       31.30        21.90        11.90        70.03        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.95        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        1.81         6.05        33.17         6.97         9.37        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
        8.98        15.02        10.98         5.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        49.51        31.30         0.39        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        18.28        55.76 

  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                         19.99                          19.99 
[1] "0.2 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   107  47
  DEL PEAK 25(10Q25.2) WILD-TYPE 339 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    107   47
  DEL PEAK 25(10Q25.2) WILD-TYPE  339  115
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON                           107                            339
  RECTUM                           47                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q25.2) MUTATED        19        0        8        42         0
  DEL PEAK 25(10Q25.2) WILD-TYPE      85        1       28       131        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q25.2) MUTATED           1         7          6         21
  DEL PEAK 25(10Q25.2) WILD-TYPE         2        19         12         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q25.2) MUTATED           18       22         6         1
  DEL PEAK 25(10Q25.2) WILD-TYPE         36       41        20         1
D52V4, multiclass
            clus
vv           DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            42                            131
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                            6                             12
  STAGE IIIB                           21                             62
  STAGE IIIC                           18                             36
  STAGE IV                             22                             41
  STAGE IVA                             6                             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 25(10Q25.2) MUTATED     3  22 115  14
  DEL PEAK 25(10Q25.2) WILD-TYPE  17  84 302  53
D52V5, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  T1                            3                             17
  T2                           22                             84
  T3                          115                            302
  T4                           14                             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 25(10Q25.2) MUTATED    74  42  38
  DEL PEAK 25(10Q25.2) WILD-TYPE 271 108  77
D52V6, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  N0                           74                            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"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   113  28
  DEL PEAK 25(10Q25.2) WILD-TYPE 337  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    113   28
  DEL PEAK 25(10Q25.2) WILD-TYPE  337   60
   clus
vv  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  0                          113                            337
  1                           28                             60
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    73  82
  DEL PEAK 25(10Q25.2) WILD-TYPE 214 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     73   82
  DEL PEAK 25(10Q25.2) WILD-TYPE  214  243
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  FEMALE                           73                            214
  MALE                             82                            243
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   108  12
  DEL PEAK 25(10Q25.2) WILD-TYPE 338  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    108   12
  DEL PEAK 25(10Q25.2) WILD-TYPE  338   16
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  NO                           108                            338
  YES                           12                             16
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                     97
  DEL PEAK 25(10Q25.2) WILD-TYPE                  285
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                               9
  DEL PEAK 25(10Q25.2) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                      39
  DEL PEAK 25(10Q25.2) WILD-TYPE                   107
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                                7
  DEL PEAK 25(10Q25.2) WILD-TYPE                              6
D52V10, multiclass
                                clus
vv                               DEL PEAK 25(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                     97
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    39
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      285
  COLON MUCINOUS ADENOCARCINOMA                              51
  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 25(10Q25.2) MUTATED   113   1  12   6
  DEL PEAK 25(10Q25.2) WILD-TYPE 329   4  25  23
D52V11, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  R0                          113                            329
  R1                            1                              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"
D52V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q25.2) MUTATED                                  0     3
  DEL PEAK 25(10Q25.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q25.2) MUTATED                          16    77
  DEL PEAK 25(10Q25.2) WILD-TYPE                        48   215
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      77
                                  clus
vv                                 DEL PEAK 25(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED     2  90
  DEL PEAK 25(10Q25.2) WILD-TYPE   3 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED      2   90
  DEL PEAK 25(10Q25.2) WILD-TYPE    3  258
                        clus
vv                       DEL PEAK 25(10Q25.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 25(10Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 26(11Q22.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11Q22.3) MUTATED    86  21
  DEL PEAK 26(11Q22.3) WILD-TYPE 386 100
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           107                            486 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                            21                            100 
$`DEL PEAK 26(11Q22.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       43.76        45.60        16.57        36.53        32.45        30.44 
TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3511 
       22.52        24.16        21.76        23.87         5.03         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3558 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3680 
        9.07        37.05        20.98         6.05         2.01        11.01 
TCGA-AA-3692 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.00        32.05        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-A00F 
        2.01        34.03         2.01        21.99        50.99        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J 
       42.02        32.02        33.04         2.96        39.98        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-A69D 
        5.79        22.42        16.44        14.50         0.95        17.85 
TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 
       19.33         1.41         2.14        12.20         1.91        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 
        5.03        15.02        15.02         2.96        11.01        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1D6 
       45.40        20.19        17.85        14.30       130.65        49.91 
TCGA-DM-A1DA TCGA-F4-6461 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
        7.50        11.11        61.91        36.00        46.75        18.18 
TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       12.79        30.28        43.04        13.55        19.10        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3591 
       15.39        10.39        32.02         7.07        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3727 TCGA-AG-3732 
       34.03         2.01         6.05        13.94         0.99        32.98 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A01W 
       19.04        17.95         1.02        13.94        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       64.01        10.98        41.00        38.56         0.69         0.72 
TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 
       10.19        12.39        13.97        10.98        19.99         5.29 
TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-7004 
       24.13        20.91        17.00        16.41         8.45 

$`DEL PEAK 26(11Q22.3) WILD-TYPE`
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-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        13.94        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       34.65        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        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-A6-6653 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-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         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-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       24.03        27.02        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        24.00        20.98        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        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-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88         0.20         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-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13       106.75        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      148.01        85.45        70.16        15.62        49.08        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95       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-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       29.06        22.03        22.98        32.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        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-D5-6926 
       15.58         1.48         3.68         4.41        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         4.80         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       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        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       47.41        35.31       133.18        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       55.04        85.48        63.62        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        79.69        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        17.85        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-2687 
        8.42        31.30        21.90        11.90        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       39.48        17.23        34.49        37.74        10.39        16.83 
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-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        8.02        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-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-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        9.07         1.02        31.00        51.98        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         1.45        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17         6.97         9.37         4.73        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        27.95         5.95         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        20.55        19.96        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46        11.97         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                          0.69                           0.00 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                        130.65                         148.01 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                        17.850                         20.485 
[1] "0.7 - 130.7 (17.9)" "0.0 - 148.0 (20.5)"
[1] "hr=" "1.2"
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    70  36
  DEL PEAK 26(11Q22.3) WILD-TYPE 376 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     70   36
  DEL PEAK 26(11Q22.3) WILD-TYPE  376  126
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON                            70                            376
  RECTUM                           36                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(11Q22.3) MUTATED        22        0        4        26         0
  DEL PEAK 26(11Q22.3) WILD-TYPE      82        1       32       147        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(11Q22.3) MUTATED           0         6          3         15
  DEL PEAK 26(11Q22.3) WILD-TYPE         3        20         15         68
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(11Q22.3) MUTATED           11       14         5         1
  DEL PEAK 26(11Q22.3) WILD-TYPE         43       49        21         1
D53V4, multiclass
            clus
vv           DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  STAGE I                              22                             82
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            26                            147
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                            3                             15
  STAGE IIIB                           15                             68
  STAGE IIIC                           11                             43
  STAGE IV                             14                             49
  STAGE IVA                             5                             21
  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(11Q22.3) MUTATED     4  19  72  15
  DEL PEAK 26(11Q22.3) WILD-TYPE  16  87 345  52
D53V5, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  T1                            4                             16
  T2                           19                             87
  T3                           72                            345
  T4                           15                             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 26(11Q22.3) MUTATED    53  32  24
  DEL PEAK 26(11Q22.3) WILD-TYPE 292 118  91
D53V6, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  N0                           53                            292
  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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    76  18
  DEL PEAK 26(11Q22.3) WILD-TYPE 374  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     76   18
  DEL PEAK 26(11Q22.3) WILD-TYPE  374   70
   clus
vv  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  0                           76                            374
  1                           18                             70
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    54  56
  DEL PEAK 26(11Q22.3) WILD-TYPE 233 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     54   56
  DEL PEAK 26(11Q22.3) WILD-TYPE  233  269
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  FEMALE                           54                            233
  MALE                             56                            269
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    79   9
  DEL PEAK 26(11Q22.3) WILD-TYPE 367  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     79    9
  DEL PEAK 26(11Q22.3) WILD-TYPE  367   19
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  NO                            79                            367
  YES                            9                             19
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                     62
  DEL PEAK 26(11Q22.3) WILD-TYPE                  320
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                               8
  DEL PEAK 26(11Q22.3) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                      29
  DEL PEAK 26(11Q22.3) WILD-TYPE                   117
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                                6
  DEL PEAK 26(11Q22.3) WILD-TYPE                              7
D53V10, multiclass
                                clus
vv                               DEL PEAK 26(11Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     62
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      320
  COLON MUCINOUS ADENOCARCINOMA                              52
  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 26(11Q22.3) MUTATED    78   0   9   4
  DEL PEAK 26(11Q22.3) WILD-TYPE 364   5  28  25
D53V11, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  R0                           78                            364
  R1                            0                              5
  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"
D53V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(11Q22.3) MUTATED                                  0     3
  DEL PEAK 26(11Q22.3) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11Q22.3) MUTATED                           6    53
  DEL PEAK 26(11Q22.3) WILD-TYPE                        58   239
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 26(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    58
  WHITE                                                       239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED     1  56
  DEL PEAK 26(11Q22.3) WILD-TYPE   4 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED      1   56
  DEL PEAK 26(11Q22.3) WILD-TYPE    4  292
                        clus
vv                       DEL PEAK 26(11Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       DEL PEAK 26(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 27(12P13.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.1) MUTATED    65  24
  DEL PEAK 27(12P13.1) WILD-TYPE 407  97
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            89                            504 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            24                             97 
$`DEL PEAK 27(12P13.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 
        4.80        43.76        24.33        45.60        34.65        36.53 
TCGA-A6-5659 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 
       30.44        24.69        20.28        61.84         9.63        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 
       14.01        33.99        13.02        78.08         2.01        50.04 
TCGA-AA-3688 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       19.00        31.07        17.03        24.03         2.01        50.99 
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-AZ-4684 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 
       65.00         2.14         0.07        49.08         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 
        2.96        29.03        15.02        11.01        11.08        10.06 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 
        1.32        15.12         1.48        11.38        13.32        12.59 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
       31.96        11.11        16.24        65.85        61.91        36.00 
TCGA-G4-6586 TCGA-NH-A50U TCGA-NH-A8F7 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2691 
       35.80        10.98        17.85        21.90        30.28        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       13.55        19.10        10.39        14.50        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3898 
       36.03        34.03        34.03        29.98        37.02        48.03 
TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A01W TCGA-AG-A026 TCGA-AH-6544 TCGA-CI-6620 
        3.98         6.02        70.03         1.94        38.56        33.17 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 
       13.97        10.98        24.13        51.48        20.91        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6641 
       16.31        16.41        28.57         0.66        26.43 

$`DEL PEAK 27(12P13.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62        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-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       13.94        16.57        37.05        37.25        37.02        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 
       34.03        29.00        29.00        12.99         0.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       15.52        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-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-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.65        32.94         5.13       106.75        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       88.21        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29        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 
        9.99        21.14        82.95         1.91       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        12.26 
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         3.68         4.41        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         4.80         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-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-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 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-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.31       133.18        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       63.62        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       13.78        26.17        91.79        46.75        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        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-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 
       11.90        70.03        24.13        39.48        17.23        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       37.74        16.83        10.39        86.63        65.98        11.84 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       12.03         6.05         0.99        15.95        19.99        13.94 
TCGA-AG-3612 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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98        15.02        27.95        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         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-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       49.51        31.30         0.39        32.19         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        12.46        18.28        55.76        47.08 

  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                         78.08                         148.01 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                         20.02                          19.99 
[1] "0.1 - 78.1 (20.0)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    59  29
  DEL PEAK 27(12P13.1) WILD-TYPE 387 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     59   29
  DEL PEAK 27(12P13.1) WILD-TYPE  387  133
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  COLON                            59                            387
  RECTUM                           29                            133
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.1) MUTATED        14        0        5        17         1
  DEL PEAK 27(12P13.1) WILD-TYPE      90        1       31       156         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.1) MUTATED           0         2          5         13
  DEL PEAK 27(12P13.1) WILD-TYPE         3        24         13         70
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(12P13.1) MUTATED           12       11         8         0
  DEL PEAK 27(12P13.1) WILD-TYPE         42       52        18         2
D54V4, multiclass
            clus
vv           DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  STAGE I                              14                             90
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            17                            156
  STAGE IIB                             1                              9
  STAGE IIC                             0                              3
  STAGE III                             2                             24
  STAGE IIIA                            5                             13
  STAGE IIIB                           13                             70
  STAGE IIIC                           12                             42
  STAGE IV                             11                             52
  STAGE IVA                             8                             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 27(12P13.1) MUTATED     4  14  65   8
  DEL PEAK 27(12P13.1) WILD-TYPE  16  92 352  59
D54V5, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  T1                            4                             16
  T2                           14                             92
  T3                           65                            352
  T4                            8                             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 27(12P13.1) MUTATED    41  32  18
  DEL PEAK 27(12P13.1) WILD-TYPE 304 118  97
D54V6, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  N0                           41                            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"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    57  19
  DEL PEAK 27(12P13.1) WILD-TYPE 393  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     57   19
  DEL PEAK 27(12P13.1) WILD-TYPE  393   69
   clus
vv  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  0                           57                            393
  1                           19                             69
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    44  47
  DEL PEAK 27(12P13.1) WILD-TYPE 243 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     44   47
  DEL PEAK 27(12P13.1) WILD-TYPE  243  278
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  FEMALE                           44                            243
  MALE                             47                            278
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    71   5
  DEL PEAK 27(12P13.1) WILD-TYPE 375  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     71    5
  DEL PEAK 27(12P13.1) WILD-TYPE  375   23
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  NO                            71                            375
  YES                            5                             23
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                     56
  DEL PEAK 27(12P13.1) WILD-TYPE                  326
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                               2
  DEL PEAK 27(12P13.1) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                      28
  DEL PEAK 27(12P13.1) WILD-TYPE                   118
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                                1
  DEL PEAK 27(12P13.1) WILD-TYPE                             12
D54V10, multiclass
                                clus
vv                               DEL PEAK 27(12P13.1) MUTATED
  COLON ADENOCARCINOMA                                     56
  COLON MUCINOUS ADENOCARCINOMA                             2
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 27(12P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      326
  COLON MUCINOUS ADENOCARCINOMA                              58
  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 27(12P13.1) MUTATED    65   1   6   4
  DEL PEAK 27(12P13.1) WILD-TYPE 377   4  31  25
D54V11, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  R0                           65                            377
  R1                            1                              4
  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"
D54V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12P13.1) MUTATED                                  0     2
  DEL PEAK 27(12P13.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12P13.1) MUTATED                          10    51
  DEL PEAK 27(12P13.1) WILD-TYPE                        54   241
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 27(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    54
  WHITE                                                       241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED     0  57
  DEL PEAK 27(12P13.1) WILD-TYPE   5 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED      0   57
  DEL PEAK 27(12P13.1) WILD-TYPE    5  291
                        clus
vv                       DEL PEAK 27(12P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           57
                        clus
vv                       DEL PEAK 27(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            291
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 28(12Q21.33) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(12Q21.33) MUTATED    63  23
  DEL PEAK 28(12Q21.33) WILD-TYPE 409  98
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             86                             507 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             23                              98 
$`DEL PEAK 28(12Q21.33) MUTATED`
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
        1.61        43.76        24.33        34.65        36.53        30.44 
TCGA-A6-5662 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3538 
       23.61        20.28        61.84        56.25         9.63        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       12.99        14.01        33.99        13.02        17.95        23.01 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 
       50.04        37.05        31.07        17.03        24.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       21.99        50.99        24.00        32.02        33.04         2.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AZ-6607 TCGA-CA-5256 
        5.79        22.42        16.44        14.50         3.19         2.14 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 
       12.20        49.08         8.02        29.06         5.03         2.96 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6533 
       29.03        15.02        11.01        13.05        11.08         1.32 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 
        4.80        11.38        12.59         7.50        31.96        16.24 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL 
       65.85        61.91        36.00        16.80         8.42        30.28 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3591 
       43.04        34.49        14.50        15.39        36.03        34.03 
TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-A00Y 
       34.03        29.98        32.98        48.03        36.03        23.01 
TCGA-AG-A014 TCGA-AG-A032 TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DE 
       15.95        38.04        38.56        13.97        10.98       129.27 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 
       24.13        17.00        16.31        16.41        11.51        28.57 
TCGA-F5-6812 TCGA-G5-6233 
        0.66        18.28 

$`DEL PEAK 28(12Q21.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80        12.66         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-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       14.53        32.45        32.91        31.63        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       16.24        24.92         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3553 
       34.03        29.00        29.00         0.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        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-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
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-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       16.08        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88         0.20         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-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.61 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69         3.06         3.25         3.29         0.07        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         9.99        21.14        82.95         1.91 
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-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        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 
       12.26        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        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-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 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-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
        8.35        82.39        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        85.48        63.62        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        74.79        79.69        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        17.85 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       42.77        29.46        32.98        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       70.03        24.13        39.48        17.23        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        10.39        16.83        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        12.00        32.02         8.02         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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
        1.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        37.02        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
        1.94        38.96        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        11.01        15.02         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       17.69        16.34         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.97         8.45         9.96        49.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                           0.66                            0.00 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         129.27                          148.01 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         22.205                          19.990 
[1] "0.7 - 129.3 (22.2)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D55V2, continuous
D55V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    61  27
  DEL PEAK 28(12Q21.33) WILD-TYPE 385 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     61   27
  DEL PEAK 28(12Q21.33) WILD-TYPE  385  135
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON                             61                             385
  RECTUM                            27                             135
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(12Q21.33) MUTATED        15        0        3        19         1
  DEL PEAK 28(12Q21.33) WILD-TYPE      89        1       33       154         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(12Q21.33) MUTATED           2         1          4         11
  DEL PEAK 28(12Q21.33) WILD-TYPE         1        25         14         72
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(12Q21.33) MUTATED           14       11         4         1
  DEL PEAK 28(12Q21.33) WILD-TYPE         40       52        22         1
D55V4, multiclass
            clus
vv           DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  STAGE I                               15                              89
  STAGE IA                               0                               1
  STAGE II                               3                              33
  STAGE IIA                             19                             154
  STAGE IIB                              1                               9
  STAGE IIC                              2                               1
  STAGE III                              1                              25
  STAGE IIIA                             4                              14
  STAGE IIIB                            11                              72
  STAGE IIIC                            14                              40
  STAGE IV                              11                              52
  STAGE IVA                              4                              22
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 28(12Q21.33) MUTATED     3  15  65   6
  DEL PEAK 28(12Q21.33) WILD-TYPE  17  91 352  61
D55V5, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  T1                             3                              17
  T2                            15                              91
  T3                            65                             352
  T4                             6                              61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 28(12Q21.33) MUTATED    42  24  23
  DEL PEAK 28(12Q21.33) WILD-TYPE 303 126  92
D55V6, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  N0                            42                             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"
D55V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    61  16
  DEL PEAK 28(12Q21.33) WILD-TYPE 389  72
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     61   16
  DEL PEAK 28(12Q21.33) WILD-TYPE  389   72
   clus
vv  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  0                            61                             389
  1                            16                              72
[1] 2 2
[1] FALSE
D55V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    39  50
  DEL PEAK 28(12Q21.33) WILD-TYPE 248 275
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     39   50
  DEL PEAK 28(12Q21.33) WILD-TYPE  248  275
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  FEMALE                            39                             248
  MALE                              50                             275
[1] 2 2
[1] FALSE
D55V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    71   5
  DEL PEAK 28(12Q21.33) WILD-TYPE 375  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     71    5
  DEL PEAK 28(12Q21.33) WILD-TYPE  375   23
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  NO                             71                             375
  YES                             5                              23
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                     58
  DEL PEAK 28(12Q21.33) WILD-TYPE                  324
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                               2
  DEL PEAK 28(12Q21.33) WILD-TYPE                            58
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                      26
  DEL PEAK 28(12Q21.33) WILD-TYPE                   120
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                                1
  DEL PEAK 28(12Q21.33) WILD-TYPE                             12
D55V10, multiclass
                                clus
vv                               DEL PEAK 28(12Q21.33) MUTATED
  COLON ADENOCARCINOMA                                      58
  COLON MUCINOUS ADENOCARCINOMA                              2
  RECTAL ADENOCARCINOMA                                     26
  RECTAL MUCINOUS ADENOCARCINOMA                             1
                                clus
vv                               DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       324
  COLON MUCINOUS ADENOCARCINOMA                               58
  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 28(12Q21.33) MUTATED    71   0   3   3
  DEL PEAK 28(12Q21.33) WILD-TYPE 371   5  34  26
D55V11, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  R0                            71                             371
  R1                             0                               5
  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"
D55V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(12Q21.33) MUTATED                                  0     2
  DEL PEAK 28(12Q21.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(12Q21.33) MUTATED                           9    47
  DEL PEAK 28(12Q21.33) WILD-TYPE                        55   245
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 28(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       47
                                  clus
vv                                 DEL PEAK 28(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     55
  WHITE                                                        245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED     1  52
  DEL PEAK 28(12Q21.33) WILD-TYPE   4 296
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED      1   52
  DEL PEAK 28(12Q21.33) WILD-TYPE    4  296
                        clus
vv                       DEL PEAK 28(12Q21.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            52
                        clus
vv                       DEL PEAK 28(12Q21.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             296
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 29(14Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(14Q11.2) MUTATED   165  39
  DEL PEAK 29(14Q11.2) WILD-TYPE 307  82
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           204                            389 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                            39                             82 
$`DEL PEAK 29(14Q11.2) MUTATED`
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-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        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-3489 
       24.69        23.87        20.28        61.84         5.03         7.04 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 
        6.97        38.99         9.07        24.03        36.03        19.07 
TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       34.03        13.02        23.01        19.99        13.94        19.99 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 
        2.01        14.01        50.04        47.01        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05        10.06        25.02        36.95        37.02        17.03 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 
       17.03        24.03        18.05        12.99        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F 
       16.08        50.99        34.06        26.01         7.96        34.03 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       38.04        27.02        42.02        14.99        21.99         1.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H 
       32.02        31.00        33.04        26.01         2.96         2.01 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       40.96         5.79        22.42        27.42        16.44        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
        0.95        33.01        17.85        18.84       109.28         1.41 
TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 
        5.65        22.36        29.56         5.23         1.61         3.06 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 
        2.14         0.07        12.20        49.08         1.91        25.02 
TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        8.02        17.03         2.96        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        11.08        10.06        45.40        12.26        56.09 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 
       18.25         1.32        15.12        14.30         4.80        11.38 
TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E 
       38.20        12.59       140.38         6.12        14.04       119.93 
TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 
       31.96        41.42        33.67        13.25         0.53        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V 
        8.35        82.39        61.91        91.79        18.18        19.33 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2689 
       15.65        17.85        16.80        30.28        11.90        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L 
       13.55        19.10        34.49        37.74        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       11.84        36.03         7.07        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       50.04         6.05         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
       17.95        17.03        35.01         1.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 
       14.04        17.03         6.02        25.97        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04        38.56        10.19         6.05        33.17 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        12.39         7.17        11.01         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        27.95        10.98         4.01         5.03       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 
       24.13        51.48        20.55        20.91        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 
       16.31        16.41        10.78        11.97        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       32.19         0.66         0.76        18.28        55.76        26.43 

$`DEL PEAK 29(14Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       15.62        12.66         1.61         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 
       43.43        42.90        24.33        44.91        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.05        37.25        37.02        31.63        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        27.09         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.18        24.16        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92        56.25         9.63         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        37.05         8.05        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       21.01        24.00        17.95        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.05         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        14.93         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-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        29.98        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
        2.01        13.05        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-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-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82        17.26        19.33        75.95        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13       106.75        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.69         3.25         3.29        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 
        9.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       12.99        14.04        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        19.59        55.92        20.19        20.42        17.75 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         1.48         3.68         4.41        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       24.43       130.65        92.75        49.91        13.32         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       44.32       131.51       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37        35.97        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-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
        1.55        34.42        16.24        47.41        35.31       133.18 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       55.04        85.48        63.62        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        74.79        79.69        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3913 
       21.90        70.03        24.13        17.23        43.04        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 
       14.50        16.83        15.39        20.02        86.63        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       46.03         2.01        12.03         0.99        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
       13.94        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-3902 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       48.03        32.02        19.99         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        13.94        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 
        0.72        26.43         1.81         6.97        78.12        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02         8.98        15.02        19.99         5.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       19.96        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        49.51        28.57 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        0.69         0.53         1.12        12.46        47.08 

  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        19.085                         20.120 
[1] "0.1 - 140.4 (19.1)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   138  68
  DEL PEAK 29(14Q11.2) WILD-TYPE 308  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    138   68
  DEL PEAK 29(14Q11.2) WILD-TYPE  308   94
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON                           138                            308
  RECTUM                           68                             94
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(14Q11.2) MUTATED        32        0       11        57         1
  DEL PEAK 29(14Q11.2) WILD-TYPE      72        1       25       116         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q11.2) MUTATED           1         9          9         29
  DEL PEAK 29(14Q11.2) WILD-TYPE         2        17          9         54
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(14Q11.2) MUTATED           18       25        12         0
  DEL PEAK 29(14Q11.2) WILD-TYPE         36       38        14         2
D56V4, multiclass
            clus
vv           DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            57                            116
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             9                             17
  STAGE IIIA                            9                              9
  STAGE IIIB                           29                             54
  STAGE IIIC                           18                             36
  STAGE IV                             25                             38
  STAGE IVA                            12                             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 29(14Q11.2) MUTATED     9  33 149  18
  DEL PEAK 29(14Q11.2) WILD-TYPE  11  73 268  49
D56V5, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           33                             73
  T3                          149                            268
  T4                           18                             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 29(14Q11.2) MUTATED   107  64  38
  DEL PEAK 29(14Q11.2) WILD-TYPE 238  86  77
D56V6, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  N0                          107                            238
  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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   149  37
  DEL PEAK 29(14Q11.2) WILD-TYPE 301  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    149   37
  DEL PEAK 29(14Q11.2) WILD-TYPE  301   51
   clus
vv  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  0                          149                            301
  1                           37                             51
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED    97 112
  DEL PEAK 29(14Q11.2) WILD-TYPE 190 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED     97  112
  DEL PEAK 29(14Q11.2) WILD-TYPE  190  213
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  FEMALE                           97                            190
  MALE                            112                            213
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   158  14
  DEL PEAK 29(14Q11.2) WILD-TYPE 288  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    158   14
  DEL PEAK 29(14Q11.2) WILD-TYPE  288   14
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  NO                           158                            288
  YES                           14                             14
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                    132
  DEL PEAK 29(14Q11.2) WILD-TYPE                  250
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                               4
  DEL PEAK 29(14Q11.2) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                      66
  DEL PEAK 29(14Q11.2) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                                2
  DEL PEAK 29(14Q11.2) WILD-TYPE                             11
D56V10, multiclass
                                clus
vv                               DEL PEAK 29(14Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    132
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      250
  COLON MUCINOUS ADENOCARCINOMA                              56
  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 29(14Q11.2) MUTATED   148   2  10  10
  DEL PEAK 29(14Q11.2) WILD-TYPE 294   3  27  19
D56V11, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  R0                          148                            294
  R1                            2                              3
  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"
D56V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(14Q11.2) MUTATED                                  0     4
  DEL PEAK 29(14Q11.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(14Q11.2) MUTATED                          22   101
  DEL PEAK 29(14Q11.2) WILD-TYPE                        42   191
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     101
                                  clus
vv                                 DEL PEAK 29(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED     2 119
  DEL PEAK 29(14Q11.2) WILD-TYPE   3 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED      2  119
  DEL PEAK 29(14Q11.2) WILD-TYPE    3  229
                        clus
vv                       DEL PEAK 29(14Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 29(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 30(14Q31.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(14Q31.1) MUTATED   169  38
  DEL PEAK 30(14Q31.1) WILD-TYPE 303  83
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           207                            386 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                            38                             83 
$`DEL PEAK 30(14Q31.1) MUTATED`
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
        4.80        39.45        43.76        42.28        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.57        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 
       30.44        23.61        22.52        24.13        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.69        23.87        20.28        61.84 
TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3526 
        5.03         6.97        38.99         9.07        24.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 
       19.07        34.03        13.02        23.01        13.94        19.99 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 
       19.00        85.05        10.06        25.02        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 
       17.03        31.07        17.03        24.03        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       12.99         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       26.01        24.00         7.96        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       14.99        21.99         1.02        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-A69D 
       27.42        16.44        14.50         0.95        33.01        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
       18.84       109.28         1.41         5.65        22.36        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
        5.23         1.61         3.06         2.14         0.07        12.20 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 
       49.08         1.91        25.02         8.02        17.03         2.96 
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        12.26        56.09        18.25         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 
       14.30         4.80        11.38        38.20        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28H TCGA-F4-6460 
        7.50       131.51        14.04       119.93       117.07        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-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 
       61.91        91.79        18.18        19.33        15.65        17.85 
TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3911 
       16.80        30.28        11.90        39.48        13.55        37.74 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       65.98        11.84        36.03        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 
       34.03        50.04        12.03         6.05         0.99        37.02 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.04         1.02        17.95        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C 
        1.02        48.03        36.03        14.04        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       25.97        23.01        70.03         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
       38.56        10.19         6.05        33.17         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       12.39         7.17        21.01        11.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG 
       27.95        10.98         4.01         5.03       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 
       20.55        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        31.30         0.39        32.19         0.66         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$`DEL PEAK 30(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       15.62        12.66         1.61         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 
       43.43        42.90        24.33        44.91        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       37.25        37.02        31.63        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        29.16        27.09         8.38        25.18 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       37.05        36.03         8.05         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       24.00        17.95        29.95        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.05         6.97        54.02         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        14.93         0.00        10.06         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-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        29.98        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       24.00        20.98        34.03         2.01        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       17.03        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        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       19.33        75.95        58.39        32.94         5.13       106.75 
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-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 
      100.01        11.74         3.19        12.69         3.25         3.29 
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         9.99        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-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-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 
       12.95        11.08        11.01        12.03        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75        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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.41        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91        12.59        44.32       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
        6.12        26.47        81.37        35.97        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-F4-6807 TCGA-F4-6855 TCGA-F4-6856 
       47.87         1.55        34.42        16.24        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18        28.21        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U 
       35.80        26.17        46.75        74.79        79.69        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33         9.93        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
        8.42        31.30        21.90        70.03        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        34.49        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       15.39        20.02        10.39        86.63        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        2.01         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 
       20.98         7.99        29.98        32.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       36.95        13.02        14.01        32.02        19.99        28.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
        1.02         3.98        46.03        20.98        13.94        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
        1.45         0.69         0.72        26.43         1.81         6.97 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       78.12        15.02         8.98        15.02        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       17.69         8.61        11.51        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        9.96        49.51        28.57         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        19.070                         20.035 
[1] "0.1 - 140.4 (19.1)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   145  68
  DEL PEAK 30(14Q31.1) WILD-TYPE 301  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    145   68
  DEL PEAK 30(14Q31.1) WILD-TYPE  301   94
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON                           145                            301
  RECTUM                           68                             94
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(14Q31.1) MUTATED        32        0        9        60         1
  DEL PEAK 30(14Q31.1) WILD-TYPE      72        1       27       113         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(14Q31.1) MUTATED           1        10          9         30
  DEL PEAK 30(14Q31.1) WILD-TYPE         2        16          9         53
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(14Q31.1) MUTATED           19       27        12         1
  DEL PEAK 30(14Q31.1) WILD-TYPE         35       36        14         1
D57V4, multiclass
            clus
vv           DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            60                            113
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            9                              9
  STAGE IIIB                           30                             53
  STAGE IIIC                           19                             35
  STAGE IV                             27                             36
  STAGE IVA                            12                             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 30(14Q31.1) MUTATED     9  33 155  18
  DEL PEAK 30(14Q31.1) WILD-TYPE  11  73 262  49
D57V5, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  T1                            9                             11
  T2                           33                             73
  T3                          155                            262
  T4                           18                             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 30(14Q31.1) MUTATED   108  65  42
  DEL PEAK 30(14Q31.1) WILD-TYPE 237  85  73
D57V6, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  N0                          108                            237
  N1                           65                             85
  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"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   153  41
  DEL PEAK 30(14Q31.1) WILD-TYPE 297  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    153   41
  DEL PEAK 30(14Q31.1) WILD-TYPE  297   47
   clus
vv  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  0                          153                            297
  1                           41                             47
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED    94 121
  DEL PEAK 30(14Q31.1) WILD-TYPE 193 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED     94  121
  DEL PEAK 30(14Q31.1) WILD-TYPE  193  204
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  FEMALE                           94                            193
  MALE                            121                            204
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   159  13
  DEL PEAK 30(14Q31.1) WILD-TYPE 287  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    159   13
  DEL PEAK 30(14Q31.1) WILD-TYPE  287   15
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  NO                           159                            287
  YES                           13                             15
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                    138
  DEL PEAK 30(14Q31.1) WILD-TYPE                  244
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                               4
  DEL PEAK 30(14Q31.1) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                      65
  DEL PEAK 30(14Q31.1) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                                1
  DEL PEAK 30(14Q31.1) WILD-TYPE                             12
D57V10, multiclass
                                clus
vv                               DEL PEAK 30(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    138
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      244
  COLON MUCINOUS ADENOCARCINOMA                              56
  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 30(14Q31.1) MUTATED   148   2  15  10
  DEL PEAK 30(14Q31.1) WILD-TYPE 294   3  22  19
D57V11, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  R0                          148                            294
  R1                            2                              3
  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"
D57V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(14Q31.1) MUTATED                                  0     4
  DEL PEAK 30(14Q31.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(14Q31.1) MUTATED                          23   100
  DEL PEAK 30(14Q31.1) WILD-TYPE                        41   192
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 30(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     100
                                  clus
vv                                 DEL PEAK 30(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED     2 119
  DEL PEAK 30(14Q31.1) WILD-TYPE   3 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED      2  119
  DEL PEAK 30(14Q31.1) WILD-TYPE    3  229
                        clus
vv                       DEL PEAK 30(14Q31.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 30(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            229
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 31(15Q11.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q11.2) MUTATED   197  46
  DEL PEAK 31(15Q11.2) WILD-TYPE 275  75
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           243                            350 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                            46                             75 
$`DEL PEAK 31(15Q11.2) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        4.80         1.61        39.45        43.76        43.43        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       42.28        44.91        45.60        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 
       32.45        32.91        30.44        29.19        29.16        22.52 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 
       25.08        20.61        21.76        20.12        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3522 
       56.25         5.03         7.04         1.02         6.97        37.05 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 
       24.00        23.01        19.99        19.99         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3821 
       47.01        37.05        19.00        36.00        85.05         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-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       12.99         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       26.01        24.00        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         1.02        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-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       33.01        17.85        18.84       106.75        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       88.21        29.56         5.23         3.19         2.14        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 
       14.30       148.01        49.08         1.91        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         2.96 
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-D5-6531 
       11.01        10.06        12.03        12.26        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
        1.32        15.12        17.13        12.49         1.48         4.41 
TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
        9.04        11.38       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
      140.38         7.50       131.51         6.12        14.04        35.97 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
       95.18        31.96        47.87         1.55        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 
       13.25         0.53        47.41        28.21         8.35        67.30 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       65.85        55.04        63.62        61.91        36.00        91.79 
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 
       30.28        11.90        24.13        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       14.50        10.39        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-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
       19.99        20.98        29.98         0.99        19.04        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       12.00        64.01         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
       38.56         0.69        10.19         6.05         9.37         4.73 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
        7.17         5.03        13.97        27.95         4.01         5.03 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
        2.40        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.69        18.28        26.43 

$`DEL PEAK 31(15Q11.2) WILD-TYPE`
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-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       35.11        13.94        37.05        37.25        37.02        14.53 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       27.09        24.13         8.38        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       24.39        23.87        19.66        16.24        24.92         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       29.00        26.01         0.99        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 
        0.99        25.02        17.98        15.95        14.93         0.00 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
        0.00        33.07         0.00        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 
       24.00         2.01        20.98        34.03        16.08        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       21.99        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
       56.55         0.79         0.72        10.88         0.20         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       27.09        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       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         9.99        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 
        3.68        12.43        14.30         9.44        11.64         4.80 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       49.91        44.32       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 
       11.11        35.74        35.74         6.18        34.42        41.42 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6304 
       35.31       133.18        82.39        23.51        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        85.48        39.42        35.93        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       18.18        19.33         9.93        15.65        17.85        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       42.77        32.98         8.42        31.30        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.23        19.10        34.49        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        86.63        36.03        12.00         8.02         7.07 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       24.00         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        13.94         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       14.01        48.03        32.02        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       46.03        20.98         6.02        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        70.03        10.98        51.98        49.97        61.97 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.72        26.43         1.81        33.17         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       12.39        78.12        21.01        11.01        15.02         8.98 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02        10.98        19.99         5.95         5.29       126.44 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       15.85        17.69        16.34        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       49.51         0.39         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                        20.190                         19.625 
[1] "0.5 - 148.0 (20.2)" "0.0 - 139.2 (19.6)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   175  74
  DEL PEAK 31(15Q11.2) WILD-TYPE 271  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    175   74
  DEL PEAK 31(15Q11.2) WILD-TYPE  271   88
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  COLON                           175                            271
  RECTUM                           74                             88
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q11.2) MUTATED        39        0        9        65         3
  DEL PEAK 31(15Q11.2) WILD-TYPE      65        1       27       108         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q11.2) MUTATED           2         9         10         35
  DEL PEAK 31(15Q11.2) WILD-TYPE         1        17          8         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q11.2) MUTATED           28       31        14         2
  DEL PEAK 31(15Q11.2) WILD-TYPE         26       32        12         0
D58V4, multiclass
            clus
vv           DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  STAGE I                              39                             65
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            65                            108
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                             9                             17
  STAGE IIIA                           10                              8
  STAGE IIIB                           35                             48
  STAGE IIIC                           28                             26
  STAGE IV                             31                             32
  STAGE IVA                            14                             12
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(15Q11.2) MUTATED     9  40 177  26
  DEL PEAK 31(15Q11.2) WILD-TYPE  11  66 240  41
D58V5, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           40                             66
  T3                          177                            240
  T4                           26                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 31(15Q11.2) MUTATED   126  72  54
  DEL PEAK 31(15Q11.2) WILD-TYPE 219  78  61
D58V6, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  N0                          126                            219
  N1                           72                             78
  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"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   177  46
  DEL PEAK 31(15Q11.2) WILD-TYPE 273  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    177   46
  DEL PEAK 31(15Q11.2) WILD-TYPE  273   42
   clus
vv  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  0                          177                            273
  1                           46                             42
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   112 140
  DEL PEAK 31(15Q11.2) WILD-TYPE 175 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    112  140
  DEL PEAK 31(15Q11.2) WILD-TYPE  175  185
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  FEMALE                          112                            175
  MALE                            140                            185
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   180  15
  DEL PEAK 31(15Q11.2) WILD-TYPE 266  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    180   15
  DEL PEAK 31(15Q11.2) WILD-TYPE  266   13
     clus
vv    DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  NO                           180                            266
  YES                           15                             13
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                    157
  DEL PEAK 31(15Q11.2) WILD-TYPE                  225
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              16
  DEL PEAK 31(15Q11.2) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                      67
  DEL PEAK 31(15Q11.2) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                6
  DEL PEAK 31(15Q11.2) WILD-TYPE                              7
D58V10, multiclass
                                clus
vv                               DEL PEAK 31(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    157
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    67
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 31(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      225
  COLON MUCINOUS ADENOCARCINOMA                              44
  RECTAL ADENOCARCINOMA                                      79
  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 31(15Q11.2) MUTATED   179   2  15   9
  DEL PEAK 31(15Q11.2) WILD-TYPE 263   3  22  20
D58V11, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  R0                          179                            263
  R1                            2                              3
  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"
D58V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(15Q11.2) MUTATED                                  1     3
  DEL PEAK 31(15Q11.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(15Q11.2) MUTATED                          25   127
  DEL PEAK 31(15Q11.2) WILD-TYPE                        39   165
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     127
                                  clus
vv                                 DEL PEAK 31(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED     2 145
  DEL PEAK 31(15Q11.2) WILD-TYPE   3 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED      2  145
  DEL PEAK 31(15Q11.2) WILD-TYPE    3  203
                        clus
vv                       DEL PEAK 31(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 31(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 32(15Q15.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q15.2) MUTATED   196  45
  DEL PEAK 32(15Q15.2) WILD-TYPE 276  76
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           241                            352 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                            45                             76 
$`DEL PEAK 32(15Q15.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 
       43.43        24.33        42.28        44.91        45.60        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-3519 TCGA-AA-3522 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        6.97         9.07        37.05        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       21.01        13.02        24.00        23.01        19.99        19.99 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 
        2.01        50.04        47.01        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       36.00        85.05        38.99        36.95        37.02        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-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.03        29.98        12.99         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F 
       13.05        34.06        24.00        27.02        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       42.02        17.03        14.99         1.02        15.02        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-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       17.85        19.33        18.84       106.75        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       88.21        29.56         5.23         3.19         2.14        12.20 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
      148.01        49.08         1.91        25.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       16.04        15.02        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       10.06        12.03        12.26        20.19         1.32        15.12 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        1.48         4.41         9.04         4.80        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       92.75        13.32        12.59       140.38       131.51         6.12 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       35.97        95.18        31.96        47.87         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       33.67        13.25         0.53        47.41        28.21         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       65.85        55.04        63.62        61.91        36.00        26.04 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW 
       91.79        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        30.28        11.90        24.13        43.04        13.55 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 
       37.74        14.50        10.39        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
       34.03         6.05        13.94        19.99        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 
       29.98        32.98         0.99        19.04        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       35.01         1.02        19.99        28.04        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
       13.94        25.97        23.01        37.02         1.02        12.00 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        1.94        38.96        41.00        38.04        38.56         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 
       10.19         6.05         9.37         4.73         7.17         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD 
       13.97        27.95         4.01         5.03        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 
       24.13        51.48         0.49         2.40        15.85        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        13.64        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 
       31.30        28.57        32.19         0.66         0.69        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 32(15Q15.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 
       12.66         9.53        46.65        42.90        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        37.02        14.53        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 
       19.66        16.24        24.92         9.63         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
        0.99        17.95        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        15.02         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        14.93         0.00         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 
       20.98        34.03        16.08        26.01        25.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        38.04         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.92        27.09        21.44        17.82        17.26       109.28 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       75.95        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.61        12.69         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       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         9.99        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         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        24.43        38.20        49.91         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 
      119.93        60.79       117.07        98.24         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 
       35.74        35.74         6.18        34.42        41.42        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      133.18        82.39        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        85.48        39.42        35.93        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        74.79        79.69        18.18 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        17.85        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       32.98         8.42        31.30        70.03        39.48        17.23 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        10.39        16.83        15.39        20.02 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 
       86.63        36.03        12.00         8.02         7.07         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-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        7.99        37.02         0.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       13.02        14.01        48.03        32.02        36.03         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 
        3.98        46.03        20.98         6.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         1.45         0.72        26.43         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       33.17         6.97        12.39        78.12        21.01        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02         8.98        15.02        10.98        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
        5.29       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         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76        12.46        55.76        47.08 

  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                          0.49                           0.00 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                         20.12                          19.81 
[1] "0.5 - 148.0 (20.1)" "0.0 - 139.2 (19.8)"
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   170  77
  DEL PEAK 32(15Q15.2) WILD-TYPE 276  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    170   77
  DEL PEAK 32(15Q15.2) WILD-TYPE  276   85
        clus
vv       DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  COLON                           170                            276
  RECTUM                           77                             85
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q15.2) MUTATED        41        0        8        62         3
  DEL PEAK 32(15Q15.2) WILD-TYPE      63        1       28       111         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q15.2) MUTATED           2        10          8         35
  DEL PEAK 32(15Q15.2) WILD-TYPE         1        16         10         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q15.2) MUTATED           27       34        13         2
  DEL PEAK 32(15Q15.2) WILD-TYPE         27       29        13         0
D59V4, multiclass
            clus
vv           DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  STAGE I                              41                             63
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            62                            111
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                            10                             16
  STAGE IIIA                            8                             10
  STAGE IIIB                           35                             48
  STAGE IIIC                           27                             27
  STAGE IV                             34                             29
  STAGE IVA                            13                             13
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 32(15Q15.2) MUTATED     9  41 175  25
  DEL PEAK 32(15Q15.2) WILD-TYPE  11  65 242  42
D59V5, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  T1                            9                             11
  T2                           41                             65
  T3                          175                            242
  T4                           25                             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 32(15Q15.2) MUTATED   123  75  52
  DEL PEAK 32(15Q15.2) WILD-TYPE 222  75  63
D59V6, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  N0                          123                            222
  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"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   171  48
  DEL PEAK 32(15Q15.2) WILD-TYPE 279  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    171   48
  DEL PEAK 32(15Q15.2) WILD-TYPE  279   40
   clus
vv  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  0                          171                            279
  1                           48                             40
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   110 140
  DEL PEAK 32(15Q15.2) WILD-TYPE 177 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    110  140
  DEL PEAK 32(15Q15.2) WILD-TYPE  177  185
        clus
vv       DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  FEMALE                          110                            177
  MALE                            140                            185
[1] 2 2
[1] FALSE
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   180  16
  DEL PEAK 32(15Q15.2) WILD-TYPE 266  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    180   16
  DEL PEAK 32(15Q15.2) WILD-TYPE  266   12
     clus
vv    DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  NO                           180                            266
  YES                           16                             12
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                    153
  DEL PEAK 32(15Q15.2) WILD-TYPE                  229
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                              15
  DEL PEAK 32(15Q15.2) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                      70
  DEL PEAK 32(15Q15.2) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                                6
  DEL PEAK 32(15Q15.2) WILD-TYPE                              7
D59V10, multiclass
                                clus
vv                               DEL PEAK 32(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                    153
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 32(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      229
  COLON MUCINOUS ADENOCARCINOMA                              45
  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 32(15Q15.2) MUTATED   180   2  16   8
  DEL PEAK 32(15Q15.2) WILD-TYPE 262   3  21  21
D59V11, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  R0                          180                            262
  R1                            2                              3
  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"
D59V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q15.2) MUTATED                                  1     2
  DEL PEAK 32(15Q15.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q15.2) MUTATED                          27   124
  DEL PEAK 32(15Q15.2) WILD-TYPE                        37   168
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     124
                                  clus
vv                                 DEL PEAK 32(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED     2 143
  DEL PEAK 32(15Q15.2) WILD-TYPE   3 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED      2  143
  DEL PEAK 32(15Q15.2) WILD-TYPE    3  205
                        clus
vv                       DEL PEAK 32(15Q15.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       DEL PEAK 32(15Q15.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            205
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 33(15Q21.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q21.1) MUTATED   195  43
  DEL PEAK 33(15Q21.1) WILD-TYPE 277  78
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           238                            355 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                            43                             78 
$`DEL PEAK 33(15Q21.1) MUTATED`
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-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 
       42.90        24.33        44.91        45.60        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       36.53        32.45        32.91        30.44        29.19        29.16 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 
       22.52        25.08        20.61        21.76        20.12        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         7.04         1.02         6.97         9.07 
TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       37.05        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 
       13.02        24.00        23.01        19.99        19.99         2.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       50.04        47.01        11.01        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       85.05        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-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.03        29.98        12.99         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00E 
       13.05        34.06        24.00        27.02        19.00        30.02 
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         1.02        15.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 
       31.00        33.04        26.01         2.96        41.00         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-A69D 
       22.42        27.42        16.44        14.50        33.01        17.85 
TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 
       18.84       106.75        65.00        62.79        88.21        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 
        5.23         3.19         2.14        12.20       148.01        49.08 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 
        1.91        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         2.96        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 
       12.26        20.19         1.32        15.12         1.48         4.41 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
        9.04         4.80        11.38       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M 
       12.59       140.38       131.51         6.12        35.97        95.18 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96        47.87         1.55        16.24        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        0.53        47.41         8.35        65.85        55.04        63.62 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       61.91        36.00        26.04        91.79        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        30.28        11.90 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 
       24.13        43.04        13.55        37.74        14.50        10.39 
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-3611 
       46.03        34.03        34.03        34.03         6.05        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99        20.98         0.99        29.98        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
       19.04        19.99        17.03        35.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        14.04        17.03        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       37.02         1.02        12.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
       38.04        38.56         0.69        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
        4.73         7.17         5.03        13.97        27.95         4.01 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.03        41.36        57.24        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        2.40        15.85        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       10.78        13.64        11.97        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69        18.28        26.43 

$`DEL PEAK 33(15Q21.1) WILD-TYPE`
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-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 
       13.94        37.05        37.25        37.02        14.53        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       23.87        19.66        16.24        24.92        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       26.01         0.99        17.95        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
        0.92        47.05        15.02         5.98         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 
       20.98        34.03        16.08        26.01        25.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00J TCGA-AA-A00K 
        7.96        27.02        13.94        38.04        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 
       38.04         4.01        27.02         0.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       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-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72        10.88         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31         0.95        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       32.94         5.13        22.36        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         1.61        12.69         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07        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         9.99        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-D5-5537 TCGA-D5-5539 
       13.02        14.04        11.01        12.95        45.40        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       56.09        55.92        20.42        17.75        18.25        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-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        3.68        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        35.74        35.74         6.18        34.42 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       41.42        35.31       133.18        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        67.30        53.62        44.68        85.48        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       35.93        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        79.69        18.18        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       17.85        16.80        42.77        32.98         8.42        31.30 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       70.03        39.48        17.23        19.10        34.49        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       16.83        15.39        20.02        86.63        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        8.02         7.07         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 
        0.99        15.95        19.99         7.99        37.02         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 
        1.02        17.95        36.95        13.02        14.01        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       32.02        36.03         1.02         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
        6.02        15.95        36.03         9.07        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       64.01        10.98        51.98        49.97        61.97         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        0.72        26.43         1.81        33.17         6.97        12.39 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       78.12        21.01        11.01        15.02         8.98        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       10.98        19.99         5.95         5.29       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-G5-6235 
        0.39         0.53         1.12         0.76        12.46        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        20.235                         19.590 
[1] "0.0 - 148.0 (20.2)" "0.0 - 139.2 (19.6)"
[1] "hr=" "1.2"
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   168  77
  DEL PEAK 33(15Q21.1) WILD-TYPE 278  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    168   77
  DEL PEAK 33(15Q21.1) WILD-TYPE  278   85
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  COLON                           168                            278
  RECTUM                           77                             85
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q21.1) MUTATED        38        0        8        65         4
  DEL PEAK 33(15Q21.1) WILD-TYPE      66        1       28       108         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q21.1) MUTATED           2        10          8         33
  DEL PEAK 33(15Q21.1) WILD-TYPE         1        16         10         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q21.1) MUTATED           26       33        13         2
  DEL PEAK 33(15Q21.1) WILD-TYPE         28       30        13         0
D60V4, multiclass
            clus
vv           DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  STAGE I                              38                             66
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            65                            108
  STAGE IIB                             4                              6
  STAGE IIC                             2                              1
  STAGE III                            10                             16
  STAGE IIIA                            8                             10
  STAGE IIIB                           33                             50
  STAGE IIIC                           26                             28
  STAGE IV                             33                             30
  STAGE IVA                            13                             13
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(15Q21.1) MUTATED     8  39 174  26
  DEL PEAK 33(15Q21.1) WILD-TYPE  12  67 243  41
D60V5, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  T1                            8                             12
  T2                           39                             67
  T3                          174                            243
  T4                           26                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 33(15Q21.1) MUTATED   124  72  51
  DEL PEAK 33(15Q21.1) WILD-TYPE 221  78  64
D60V6, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  N0                          124                            221
  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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   170  47
  DEL PEAK 33(15Q21.1) WILD-TYPE 280  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    170   47
  DEL PEAK 33(15Q21.1) WILD-TYPE  280   41
   clus
vv  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  0                          170                            280
  1                           47                             41
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   107 140
  DEL PEAK 33(15Q21.1) WILD-TYPE 180 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    107  140
  DEL PEAK 33(15Q21.1) WILD-TYPE  180  185
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  FEMALE                          107                            180
  MALE                            140                            185
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   176  16
  DEL PEAK 33(15Q21.1) WILD-TYPE 270  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    176   16
  DEL PEAK 33(15Q21.1) WILD-TYPE  270   12
     clus
vv    DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  NO                           176                            270
  YES                           16                             12
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                    151
  DEL PEAK 33(15Q21.1) WILD-TYPE                  231
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                              15
  DEL PEAK 33(15Q21.1) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                      70
  DEL PEAK 33(15Q21.1) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                                6
  DEL PEAK 33(15Q21.1) WILD-TYPE                              7
D60V10, multiclass
                                clus
vv                               DEL PEAK 33(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 33(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      231
  COLON MUCINOUS ADENOCARCINOMA                              45
  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(15Q21.1) MUTATED   178   1  16   8
  DEL PEAK 33(15Q21.1) WILD-TYPE 264   4  21  21
D60V11, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  R0                          178                            264
  R1                            1                              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"
D60V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q21.1) MUTATED                                  1     2
  DEL PEAK 33(15Q21.1) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q21.1) MUTATED                          23   122
  DEL PEAK 33(15Q21.1) WILD-TYPE                        41   170
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     122
                                  clus
vv                                 DEL PEAK 33(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED     2 137
  DEL PEAK 33(15Q21.1) WILD-TYPE   3 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED      2  137
  DEL PEAK 33(15Q21.1) WILD-TYPE    3  211
                        clus
vv                       DEL PEAK 33(15Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          137
                        clus
vv                       DEL PEAK 33(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            211
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 34(15Q22.33) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(15Q22.33) MUTATED   186  43
  DEL PEAK 34(15Q22.33) WILD-TYPE 286  78
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            229                             364 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                             43                              78 
$`DEL PEAK 34(15Q22.33) MUTATED`
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-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       24.33        44.91        45.60        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.45        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       20.61        21.76        20.28        61.84         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        1.02         6.97         9.07        37.05        29.00        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       33.99        21.01        13.02        23.01        19.99        19.99 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
        2.01        50.04        37.05        19.00        36.00        85.05 
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-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 
       31.07        17.03        24.03        29.98        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 
       21.99        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99         1.02 
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-AM-5820 TCGA-AU-3779 
        5.79        22.42        27.42        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 
       16.31         0.95        33.01        17.85        18.84       106.75 
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-5912 TCGA-CK-6748 TCGA-CM-4747 
        2.14        12.20       148.01        49.08         1.91        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 
        2.96        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         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         1.48         4.41         9.04         4.80 
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-A285 TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 
      140.38       131.51         6.12        14.04        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        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       47.41         8.35        65.85        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC 
       36.00        91.79        46.75        10.98        19.33        12.79 
TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 
       29.46         8.42        21.90        30.28        11.90        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 
       43.04        13.55        34.49        37.74        14.50        10.39 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 
       65.98        32.02        36.03        20.05        24.00        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
       34.03         6.05        15.95        13.94        19.99        20.98 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 
       29.98         0.99        19.04        19.99        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
        1.02        19.99        28.04        14.04        17.03        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       25.97        23.01        37.02         1.02        12.00        70.03 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       38.96        41.00        38.04        38.56         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 
        6.05         9.37         7.17        21.01         5.03        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       27.95         4.01         5.03        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 
       24.13        51.48         0.49         2.40        15.85        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 
       16.41        11.51        10.78        13.64        11.97        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 
       28.57        32.19         0.66         0.69        12.46        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 34(15Q22.33) WILD-TYPE`
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-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 
       35.11        13.94        37.05        37.25        37.02        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        24.13         8.38        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       24.92        56.25         9.63         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
        1.02        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        26.01         0.99        14.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       24.00        17.95        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-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-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        14.93         0.00 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       16.08        26.01        25.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        4.01        27.02         0.99        21.99        34.98        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-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37        15.52        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
        0.72        10.88         0.20         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82        17.26        19.33       109.28        75.95        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
        1.41         5.65        32.94         5.13        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07        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-6751 TCGA-CM-4743 TCGA-CM-4744 
        9.99        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04         8.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 
       32.02        15.02        15.02        15.02        12.00        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       13.05        45.40        12.26        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-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         3.68        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       38.20         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       34.42        41.42        35.31       133.18        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        74.79        79.69        18.18        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        17.85        16.80        42.77        32.98 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 
       31.30        70.03        39.48        17.23        19.10        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        15.39        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       12.00         8.02         7.07         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 
        2.01        50.04        12.03         0.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 
        0.99        37.02        32.98         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-A014 
        1.02         3.98        46.03        20.98         6.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       49.97         1.94        61.97         1.45         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.81        33.17         6.97         4.73        12.39        78.12 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       11.01        15.02         8.98        15.02        10.98        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
        5.95         5.29       126.44        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        17.00        18.28        17.69        16.34         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 
       17.46         8.45         9.96        49.51         0.39         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        55.76        47.08 

  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                           0.46                            0.00 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                         148.01                          139.17 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                          19.99                           19.99 
[1] "0.5 - 148.0 (20.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   159  75
  DEL PEAK 34(15Q22.33) WILD-TYPE 287  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    159   75
  DEL PEAK 34(15Q22.33) WILD-TYPE  287   87
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  COLON                            159                             287
  RECTUM                            75                              87
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(15Q22.33) MUTATED        32        0        7        62         3
  DEL PEAK 34(15Q22.33) WILD-TYPE      72        1       29       111         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q22.33) MUTATED           2         8          9         34
  DEL PEAK 34(15Q22.33) WILD-TYPE         1        18          9         49
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(15Q22.33) MUTATED           28       32        14         1
  DEL PEAK 34(15Q22.33) WILD-TYPE         26       31        12         1
D61V4, multiclass
            clus
vv           DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  STAGE I                               32                              72
  STAGE IA                               0                               1
  STAGE II                               7                              29
  STAGE IIA                             62                             111
  STAGE IIB                              3                               7
  STAGE IIC                              2                               1
  STAGE III                              8                              18
  STAGE IIIA                             9                               9
  STAGE IIIB                            34                              49
  STAGE IIIC                            28                              26
  STAGE IV                              32                              31
  STAGE IVA                             14                              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 34(15Q22.33) MUTATED     9  31 174  23
  DEL PEAK 34(15Q22.33) WILD-TYPE  11  75 243  44
D61V5, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  T1                             9                              11
  T2                            31                              75
  T3                           174                             243
  T4                            23                              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 34(15Q22.33) MUTATED   114  69  54
  DEL PEAK 34(15Q22.33) WILD-TYPE 231  81  61
D61V6, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  N0                           114                             231
  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"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   161  46
  DEL PEAK 34(15Q22.33) WILD-TYPE 289  42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    161   46
  DEL PEAK 34(15Q22.33) WILD-TYPE  289   42
   clus
vv  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  0                           161                             289
  1                            46                              42
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   105 132
  DEL PEAK 34(15Q22.33) WILD-TYPE 182 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    105  132
  DEL PEAK 34(15Q22.33) WILD-TYPE  182  193
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  FEMALE                           105                             182
  MALE                             132                             193
[1] 2 2
[1] FALSE
D61V9, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   168  15
  DEL PEAK 34(15Q22.33) WILD-TYPE 278  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    168   15
  DEL PEAK 34(15Q22.33) WILD-TYPE  278   13
     clus
vv    DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  NO                            168                             278
  YES                            15                              13
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                    143
  DEL PEAK 34(15Q22.33) WILD-TYPE                  239
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                              14
  DEL PEAK 34(15Q22.33) WILD-TYPE                            46
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                      68
  DEL PEAK 34(15Q22.33) WILD-TYPE                    78
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                                6
  DEL PEAK 34(15Q22.33) WILD-TYPE                              7
D61V10, multiclass
                                clus
vv                               DEL PEAK 34(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                     143
  COLON MUCINOUS ADENOCARCINOMA                             14
  RECTAL ADENOCARCINOMA                                     68
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 34(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       239
  COLON MUCINOUS ADENOCARCINOMA                               46
  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 34(15Q22.33) MUTATED   170   1  15   8
  DEL PEAK 34(15Q22.33) WILD-TYPE 272   4  22  21
D61V11, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  R0                           170                             272
  R1                             1                               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"
D61V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(15Q22.33) MUTATED                                  1     2
  DEL PEAK 34(15Q22.33) WILD-TYPE                                0    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(15Q22.33) MUTATED                          23   124
  DEL PEAK 34(15Q22.33) WILD-TYPE                        41   168
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 34(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      124
                                  clus
vv                                 DEL PEAK 34(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     41
  WHITE                                                        168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED     2 139
  DEL PEAK 34(15Q22.33) WILD-TYPE   3 209
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED      2  139
  DEL PEAK 34(15Q22.33) WILD-TYPE    3  209
                        clus
vv                       DEL PEAK 34(15Q22.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           139
                        clus
vv                       DEL PEAK 34(15Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             209
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 35(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16P13.3) MUTATED    45  20
  DEL PEAK 35(16P13.3) WILD-TYPE 427 101
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            65                            528 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            20                            101 
$`DEL PEAK 35(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 
       24.33        44.91        45.60        34.65        14.53        21.76 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 
       61.84         5.03        13.02        54.02        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 
       36.95        31.07         2.01        33.01         2.01         2.01 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F TCGA-AA-A02Y TCGA-AD-A5EK 
       27.02        34.03        27.02        39.98        39.98        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 
        0.46        14.50        16.31        17.85         5.65         3.19 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6165 
       13.02        22.03        22.98         5.03        15.02        16.04 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1D6 
       13.02        11.01        11.01        20.19        17.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 TCGA-G4-6294 TCGA-G4-6626 TCGA-NH-A50T 
       12.59        44.32         8.61        28.21        46.75        18.18 
TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-AG-3578 TCGA-AG-3591 
       10.98        42.77        30.28        11.90        32.02        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3881 TCGA-AG-4005 TCGA-AG-A02G 
        6.05        19.99         7.99        19.04        14.04        38.96 
TCGA-DC-6682 TCGA-EI-6882 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        4.01         8.61        32.19         0.53        18.28 

$`DEL PEAK 35(16P13.3) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        13.94        16.57        37.05        37.25        37.02 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         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-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98         1.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
        2.96         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.20         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-4313 
       17.82        17.26        19.33        18.84       109.28        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13       106.75        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.61        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32         9.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         1.91       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 
       25.02        26.04         8.02        27.02        29.06        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
        2.96        29.03        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        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         1.32        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         1.48 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        3.68         4.41        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         4.80         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-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        16.24        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       35.31       133.18         8.35        82.39        23.51        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       63.62        39.42        35.93        61.91        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        79.69        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        36.03        12.00         8.02         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-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       13.94        19.99        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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.97         1.94        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         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         5.03         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30        28.57         0.39         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76        12.46        55.76        47.08        26.43 

  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         61.84                         148.01 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         18.28                          20.02 
[1] "0.5 - 61.8 (18.3)"  "0.0 - 148.0 (20.0)"
[1] "hr=" "1.9"
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    55  13
  DEL PEAK 35(16P13.3) WILD-TYPE 391 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     55   13
  DEL PEAK 35(16P13.3) WILD-TYPE  391  149
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  COLON                            55                            391
  RECTUM                           13                            149
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(16P13.3) MUTATED         4        0        3        24         2
  DEL PEAK 35(16P13.3) WILD-TYPE     100        1       33       149         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(16P13.3) MUTATED           1         0          0          9
  DEL PEAK 35(16P13.3) WILD-TYPE         2        26         18         74
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(16P13.3) MUTATED           11        8         5         0
  DEL PEAK 35(16P13.3) WILD-TYPE         43       55        21         2
D62V4, multiclass
            clus
vv           DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  STAGE I                               4                            100
  STAGE IA                              0                              1
  STAGE II                              3                             33
  STAGE IIA                            24                            149
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             0                             26
  STAGE IIIA                            0                             18
  STAGE IIIB                            9                             74
  STAGE IIIC                           11                             43
  STAGE IV                              8                             55
  STAGE IVA                             5                             21
  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 35(16P13.3) MUTATED     0   6  55   7
  DEL PEAK 35(16P13.3) WILD-TYPE  20 100 362  60
D62V5, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  T1                            0                             20
  T2                            6                            100
  T3                           55                            362
  T4                            7                             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 35(16P13.3) MUTATED    34  16  18
  DEL PEAK 35(16P13.3) WILD-TYPE 311 134  97
D62V6, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  N0                           34                            311
  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"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    46  13
  DEL PEAK 35(16P13.3) WILD-TYPE 404  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     46   13
  DEL PEAK 35(16P13.3) WILD-TYPE  404   75
   clus
vv  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  0                           46                            404
  1                           13                             75
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    30  38
  DEL PEAK 35(16P13.3) WILD-TYPE 257 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     30   38
  DEL PEAK 35(16P13.3) WILD-TYPE  257  287
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  FEMALE                           30                            257
  MALE                             38                            287
[1] 2 2
[1] FALSE
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    54   2
  DEL PEAK 35(16P13.3) WILD-TYPE 392  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     54    2
  DEL PEAK 35(16P13.3) WILD-TYPE  392   26
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  NO                            54                            392
  YES                            2                             26
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                     48
  DEL PEAK 35(16P13.3) WILD-TYPE                  334
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                               7
  DEL PEAK 35(16P13.3) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                      10
  DEL PEAK 35(16P13.3) WILD-TYPE                   136
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                                2
  DEL PEAK 35(16P13.3) WILD-TYPE                             11
D62V10, multiclass
                                clus
vv                               DEL PEAK 35(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                     48
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 35(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      334
  COLON MUCINOUS ADENOCARCINOMA                              53
  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 35(16P13.3) MUTATED    51   1   4   1
  DEL PEAK 35(16P13.3) WILD-TYPE 391   4  33  28
D62V11, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  R0                           51                            391
  R1                            1                              4
  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"
D62V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(16P13.3) MUTATED                                  0     0
  DEL PEAK 35(16P13.3) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(16P13.3) MUTATED                          11    32
  DEL PEAK 35(16P13.3) WILD-TYPE                        53   260
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 35(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 35(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    53
  WHITE                                                       260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED     1  41
  DEL PEAK 35(16P13.3) WILD-TYPE   4 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED      1   41
  DEL PEAK 35(16P13.3) WILD-TYPE    4  307
                        clus
vv                       DEL PEAK 35(16P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK 35(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            307
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 36(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16Q23.1) MUTATED    62  20
  DEL PEAK 36(16Q23.1) WILD-TYPE 410 101
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            82                            511 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            20                            101 
$`DEL PEAK 36(16Q23.1) MUTATED`
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-5660 
        1.61        43.76        42.90        42.28        45.60        29.19 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-A565 
       33.53        22.06        22.52        21.76        24.39        16.24 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3549 
        1.02         6.97        13.02         1.02         0.99        21.01 
TCGA-AA-3672 TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3860 
        0.92        37.05        17.98        38.99        36.03        31.07 
TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E TCGA-AA-A00J 
       53.00        33.01         2.01        21.99        30.02        18.05 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-A5EK 
       38.07         1.02         2.96        22.03        41.00        16.44 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 
       17.85         5.65         5.13        49.41        12.10         3.19 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6169 
       12.69         3.29        22.03         5.03        15.02        13.02 
TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DA 
       11.01        20.19        17.75        15.12        24.43         7.50 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-6672 
       18.18        10.98        31.30        30.28        11.90        10.39 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 
       32.02        36.03        34.03         6.05        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-4005 TCGA-AH-6544 
        7.99        32.98        19.04         1.02        14.04        38.56 
TCGA-AH-6644 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 TCGA-EI-7004 
        0.72         4.01       129.27        11.51        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        9.96        32.19         0.53        18.28 

$`DEL PEAK 36(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       15.62         4.80        12.66         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
       43.76        43.43        24.33        44.91        35.11        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       16.57        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 
       14.53        32.45        32.91        31.63        30.44        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        24.16        20.61        24.69        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        20.28        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       35.01        58.03        63.98         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-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-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F 
        7.96        27.02        13.94        38.04        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98         1.02        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-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       51.98        39.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37        15.52        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84       109.28        75.95        58.39         1.41        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
      106.75        22.36        65.00        62.79        88.21         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 
      100.01        29.56         5.23        11.74         1.61         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         0.07        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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        51.32         9.99        21.14        82.95         1.91 
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-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        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 
        2.96        29.03        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-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25         1.32        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-D5-6924 TCGA-D5-6926 
        1.48         3.68         4.41        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         4.80         1.51        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-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       13.25         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        85.48        63.62        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        61.91        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       79.69        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        15.39        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         8.02         7.07        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-3611 TCGA-AG-3612 TCGA-AG-3727 
       12.03         0.99        15.95        13.94        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       29.98        37.02         0.99         0.99        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         1.45         0.69        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       17.46        49.51        31.30        28.57         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.76        12.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                          0.53                           0.00 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        18.015                         20.120 
[1] "0.5 - 129.3 (18.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.7"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    60  23
  DEL PEAK 36(16Q23.1) WILD-TYPE 386 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     60   23
  DEL PEAK 36(16Q23.1) WILD-TYPE  386  139
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  COLON                            60                            386
  RECTUM                           23                            139
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(16Q23.1) MUTATED        13        0        5        25         2
  DEL PEAK 36(16Q23.1) WILD-TYPE      91        1       31       148         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16Q23.1) MUTATED           2         4          0          8
  DEL PEAK 36(16Q23.1) WILD-TYPE         1        22         18         75
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(16Q23.1) MUTATED            6       11         5         0
  DEL PEAK 36(16Q23.1) WILD-TYPE         48       52        21         2
D63V4, multiclass
            clus
vv           DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  STAGE I                              13                             91
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            25                            148
  STAGE IIB                             2                              8
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            0                             18
  STAGE IIIB                            8                             75
  STAGE IIIC                            6                             48
  STAGE IV                             11                             52
  STAGE IVA                             5                             21
  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(16Q23.1) MUTATED     0  14  57  12
  DEL PEAK 36(16Q23.1) WILD-TYPE  20  92 360  55
D63V5, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  T1                            0                             20
  T2                           14                             92
  T3                           57                            360
  T4                           12                             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 36(16Q23.1) MUTATED    49  16  17
  DEL PEAK 36(16Q23.1) WILD-TYPE 296 134  98
D63V6, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  N0                           49                            296
  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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    58  15
  DEL PEAK 36(16Q23.1) WILD-TYPE 392  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     58   15
  DEL PEAK 36(16Q23.1) WILD-TYPE  392   73
   clus
vv  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  0                           58                            392
  1                           15                             73
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    42  41
  DEL PEAK 36(16Q23.1) WILD-TYPE 245 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     42   41
  DEL PEAK 36(16Q23.1) WILD-TYPE  245  284
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  FEMALE                           42                            245
  MALE                             41                            284
[1] 2 2
[1] FALSE
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    64   4
  DEL PEAK 36(16Q23.1) WILD-TYPE 382  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     64    4
  DEL PEAK 36(16Q23.1) WILD-TYPE  382   24
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  NO                            64                            382
  YES                            4                             24
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                     50
  DEL PEAK 36(16Q23.1) WILD-TYPE                  332
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                              10
  DEL PEAK 36(16Q23.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                      20
  DEL PEAK 36(16Q23.1) WILD-TYPE                   126
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                                2
  DEL PEAK 36(16Q23.1) WILD-TYPE                             11
D63V10, multiclass
                                clus
vv                               DEL PEAK 36(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                     50
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 36(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      332
  COLON MUCINOUS ADENOCARCINOMA                              50
  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 36(16Q23.1) MUTATED    58   0   3   4
  DEL PEAK 36(16Q23.1) WILD-TYPE 384   5  34  25
D63V11, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  R0                           58                            384
  R1                            0                              5
  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"
D63V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(16Q23.1) MUTATED                                  0     2
  DEL PEAK 36(16Q23.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16Q23.1) MUTATED                          13    34
  DEL PEAK 36(16Q23.1) WILD-TYPE                        51   258
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 36(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 36(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED     2  44
  DEL PEAK 36(16Q23.1) WILD-TYPE   3 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED      2   44
  DEL PEAK 36(16Q23.1) WILD-TYPE    3  304
                        clus
vv                       DEL PEAK 36(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       DEL PEAK 36(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            304
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 37(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(17P12) MUTATED   282  73
  DEL PEAK 37(17P12) WILD-TYPE 190  48
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         355                          238 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                          73                           48 
$`DEL PEAK 37(17P12) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
       15.62         4.80         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       43.43        24.33        42.28        35.11        45.60        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       31.63        30.44        29.19        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       22.52        24.13        25.18        24.16        20.61        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       23.87        20.28        61.84         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 
       37.05         1.02         6.97         1.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
       24.03        37.05        36.03        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       36.00        85.05        10.06        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       37.02        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       50.99        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       19.00        34.03        38.04        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       31.00         1.02        33.04        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
        2.01         5.03        41.00        40.96        21.37        15.52 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         5.79        22.42        27.42         0.20        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D 
        0.46        14.50        16.31         0.95        33.01        17.85 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
      109.28         1.41         5.65         5.13       106.75        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-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         2.14         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
       14.30       148.01        49.08         9.99         1.91        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        8.02        27.02        13.02        29.06        22.03         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        17.03        29.03        21.99        14.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       13.02        15.02        11.01        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       45.40        12.26        19.59        56.09        55.92        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       18.25         1.32        43.27        15.12        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         1.48         4.41        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        4.80        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
        6.12        14.04        26.47       119.93        35.97       117.07 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       31.96        11.11        34.42        16.24        33.67        13.25 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
        8.35        23.51        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 
       39.42        35.93        61.91        36.00        26.43        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        10.98        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       17.85        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       21.90        30.28        11.90        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        34.49        37.74        14.50        15.39 
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-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        36.03        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03         2.01        50.04         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       19.99        13.94        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 
       32.98         0.99        19.04         1.02        17.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A008 
       36.03        14.04         1.02        17.03         3.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        15.95         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       12.00        31.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04        38.56         0.69         0.72        26.43 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 
       10.19         6.05        33.17         6.97        12.39         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       21.01        11.01        13.97        15.02        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       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         0.49         2.40        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        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39         0.69         0.53         0.76        12.46 
TCGA-G5-6235 
       55.76 

$`DEL PEAK 37(17P12) WILD-TYPE`
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 
       12.66         9.53        46.65        42.90        44.91        13.94 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       37.02        36.53        33.53        23.61        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        25.08        21.76        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 
       16.24        24.92        56.25         9.63         3.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 
       58.03        63.98        13.02         1.02         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        15.02        11.01         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       14.93         0.00        17.03         0.00         0.00        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       24.00         2.01        13.05        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        34.98         1.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O 
       35.01        35.01        26.01        39.06        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.03        39.98        18.05         0.07        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       10.88         0.92        27.09        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 
       19.33        18.84        75.95        58.39        32.94        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       49.41         6.77       100.01        11.74         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       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         2.96        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         3.68         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA 
        1.51        12.00        10.26       119.70        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
      135.65         7.76        81.37        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        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-G4-6294 
       41.42         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       82.39        74.56        67.30        53.62        85.48        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        74.79        79.69 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 
       18.18        19.33        31.30        70.03        24.13        10.39 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3592 TCGA-AG-3599 
       16.83        10.39         8.02        20.05        34.03        12.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        6.05        19.99        29.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 
       13.02        14.01        46.03        20.98        36.03         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 
       10.98        49.97        38.96        61.97         1.45         1.81 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        9.37         4.73        78.12        15.02         5.03         8.98 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 
       27.95         5.95        32.61        20.55        19.96        15.85 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 
        8.61        11.51        13.64        17.46        32.19         0.66 
TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        1.12        18.28        47.08        26.43 

  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                      148.01                       135.65 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                       19.99                        19.99 
[1] "0.1 - 148.0 (20.0)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   250 113
  DEL PEAK 37(17P12) WILD-TYPE 196  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    250  113
  DEL PEAK 37(17P12) WILD-TYPE  196   49
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  COLON                         250                          196
  RECTUM                        113                           49
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(17P12) MUTATED        53        0       19        89         3
  DEL PEAK 37(17P12) WILD-TYPE      51        1       17        84         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17P12) MUTATED           1        17         14         54
  DEL PEAK 37(17P12) WILD-TYPE         2         9          4         29
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(17P12) MUTATED           41       46        20         2
  DEL PEAK 37(17P12) WILD-TYPE         13       17         6         0
D64V4, multiclass
            clus
vv           DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  STAGE I                            53                           51
  STAGE IA                            0                            1
  STAGE II                           19                           17
  STAGE IIA                          89                           84
  STAGE IIB                           3                            7
  STAGE IIC                           1                            2
  STAGE III                          17                            9
  STAGE IIIA                         14                            4
  STAGE IIIB                         54                           29
  STAGE IIIC                         41                           13
  STAGE IV                           46                           17
  STAGE IVA                          20                            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 37(17P12) MUTATED     9  60 256  42
  DEL PEAK 37(17P12) WILD-TYPE  11  46 161  25
D64V5, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  T1                          9                           11
  T2                         60                           46
  T3                        256                          161
  T4                         42                           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 37(17P12) MUTATED   180 103  83
  DEL PEAK 37(17P12) WILD-TYPE 165  47  32
D64V6, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  N0                        180                          165
  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"
D64V7, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   260  66
  DEL PEAK 37(17P12) WILD-TYPE 190  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    260   66
  DEL PEAK 37(17P12) WILD-TYPE  190   22
   clus
vv  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  0                        260                          190
  1                         66                           22
[1] 2 2
[1] FALSE
D64V8, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   167 200
  DEL PEAK 37(17P12) WILD-TYPE 120 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    167  200
  DEL PEAK 37(17P12) WILD-TYPE  120  125
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  FEMALE                        167                          120
  MALE                          200                          125
[1] 2 2
[1] FALSE
D64V9, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   268  17
  DEL PEAK 37(17P12) WILD-TYPE 178  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    268   17
  DEL PEAK 37(17P12) WILD-TYPE  178   11
     clus
vv    DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  NO                         268                          178
  YES                         17                           11
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                    231
  DEL PEAK 37(17P12) WILD-TYPE                  151
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                              16
  DEL PEAK 37(17P12) WILD-TYPE                            44
                              vv
clus                           RECTAL ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                     105
  DEL PEAK 37(17P12) WILD-TYPE                    41
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                                6
  DEL PEAK 37(17P12) WILD-TYPE                              7
D64V10, multiclass
                                clus
vv                               DEL PEAK 37(17P12) MUTATED
  COLON ADENOCARCINOMA                                  231
  COLON MUCINOUS ADENOCARCINOMA                          16
  RECTAL ADENOCARCINOMA                                 105
  RECTAL MUCINOUS ADENOCARCINOMA                          6
                                clus
vv                               DEL PEAK 37(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            44
  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 37(17P12) MUTATED   261   3  26  13
  DEL PEAK 37(17P12) WILD-TYPE 181   2  11  16
D64V11, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  R0                        261                          181
  R1                          3                            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"
D64V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(17P12) MUTATED                                  0     7
  DEL PEAK 37(17P12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(17P12) MUTATED                          38   175
  DEL PEAK 37(17P12) WILD-TYPE                        26   117
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 37(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                38
  WHITE                                                   175
                                  clus
vv                                 DEL PEAK 37(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED     4 205
  DEL PEAK 37(17P12) WILD-TYPE   1 143
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED      4  205
  DEL PEAK 37(17P12) WILD-TYPE    1  143
                        clus
vv                       DEL PEAK 37(17P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        205
                        clus
vv                       DEL PEAK 37(17P12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          143
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 38(17Q24.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(17Q24.3) MUTATED    69  24
  DEL PEAK 38(17Q24.3) WILD-TYPE 403  97
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            93                            500 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            24                             97 
$`DEL PEAK 38(17Q24.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 
       43.76        43.76        37.05        32.45        31.63        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 
       25.18        24.16        24.03        12.99        21.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 
        6.05         2.01        50.04        37.05        19.00        10.06 
TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3989 
       37.02        31.07        27.02        24.00        26.01         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       34.03        42.02        10.98        32.02        33.04         2.96 
TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-A69D TCGA-AY-A8YK 
       39.98         5.79        22.42         0.20        17.85        18.84 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4751 
       12.10         3.29        12.20        49.08        25.02        27.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 
        5.03        15.02        15.02        45.40        43.27        12.49 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 
        4.80        11.38        38.20       130.65        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       44.32         7.76       117.07        31.96        35.74         1.55 
TCGA-F4-6809 TCGA-G4-6295 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV 
       13.25         8.35        10.98         9.93        12.79        42.77 
TCGA-QL-A97D TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 
       21.90        14.50        15.39        65.98         7.07        36.03 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3611 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 
        1.02        34.03        13.94         1.02        32.02        28.04 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6643 
       13.94        25.97         9.07        12.00        41.00         0.69 
TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF 
       10.19        13.97        15.02        10.98         5.29        24.13 
TCGA-EI-6508 TCGA-EI-6881 TCGA-F5-6814 
       20.91        16.41         0.53 

$`DEL PEAK 38(17Q24.3) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.43        42.90        24.33        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        14.53        32.91        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       27.09        24.13         8.38        25.08        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       34.06        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         1.02        15.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        51.98         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-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        10.88        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.61        12.69         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.14         3.25         0.07        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 
        9.99        21.14        82.95         1.91       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         2.96        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        12.26        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         1.32        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         1.48         3.68 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        4.41        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 
        1.51        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-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        47.41        35.31       133.18        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        85.48        63.62        39.42        35.93        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        74.79        79.69        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33        15.65        17.85        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        30.28        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        10.39        16.83        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        11.84        36.03        12.00        32.02         8.02 
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-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        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-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        46.03        20.98         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         1.02        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         1.45         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
        8.98        27.95        19.99         5.95         4.01         5.03 
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-6509 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         1.12         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                         19.99                          19.99 
[1] "0.2 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.5"
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    69  25
  DEL PEAK 38(17Q24.3) WILD-TYPE 377 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     69   25
  DEL PEAK 38(17Q24.3) WILD-TYPE  377  137
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON                            69                            377
  RECTUM                           25                            137
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(17Q24.3) MUTATED        15        0        5        15         0
  DEL PEAK 38(17Q24.3) WILD-TYPE      89        1       31       158        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17Q24.3) MUTATED           0         4          5         11
  DEL PEAK 38(17Q24.3) WILD-TYPE         3        22         13         72
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(17Q24.3) MUTATED           15       12         9         1
  DEL PEAK 38(17Q24.3) WILD-TYPE         39       51        17         1
D65V4, multiclass
            clus
vv           DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  STAGE I                              15                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            15                            158
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            5                             13
  STAGE IIIB                           11                             72
  STAGE IIIC                           15                             39
  STAGE IV                             12                             51
  STAGE IVA                             9                             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
  DEL PEAK 38(17Q24.3) MUTATED     0  19  62  14
  DEL PEAK 38(17Q24.3) WILD-TYPE  20  87 355  53
D65V5, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  T1                            0                             20
  T2                           19                             87
  T3                           62                            355
  T4                           14                             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 38(17Q24.3) MUTATED    38  30  27
  DEL PEAK 38(17Q24.3) WILD-TYPE 307 120  88
D65V6, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  N0                           38                            307
  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"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    59  21
  DEL PEAK 38(17Q24.3) WILD-TYPE 391  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     59   21
  DEL PEAK 38(17Q24.3) WILD-TYPE  391   67
   clus
vv  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  0                           59                            391
  1                           21                             67
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    39  56
  DEL PEAK 38(17Q24.3) WILD-TYPE 248 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     39   56
  DEL PEAK 38(17Q24.3) WILD-TYPE  248  269
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  FEMALE                           39                            248
  MALE                             56                            269
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    68   5
  DEL PEAK 38(17Q24.3) WILD-TYPE 378  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     68    5
  DEL PEAK 38(17Q24.3) WILD-TYPE  378   23
     clus
vv    DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  NO                            68                            378
  YES                            5                             23
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                     59
  DEL PEAK 38(17Q24.3) WILD-TYPE                  323
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                               9
  DEL PEAK 38(17Q24.3) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                      22
  DEL PEAK 38(17Q24.3) WILD-TYPE                   124
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                                2
  DEL PEAK 38(17Q24.3) WILD-TYPE                             11
D65V10, multiclass
                                clus
vv                               DEL PEAK 38(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                     59
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    22
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      323
  COLON MUCINOUS ADENOCARCINOMA                              51
  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 38(17Q24.3) MUTATED    63   0   8   6
  DEL PEAK 38(17Q24.3) WILD-TYPE 379   5  29  23
D65V11, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  R0                           63                            379
  R1                            0                              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"
D65V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(17Q24.3) MUTATED                                  1     3
  DEL PEAK 38(17Q24.3) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17Q24.3) MUTATED                          10    45
  DEL PEAK 38(17Q24.3) WILD-TYPE                        54   247
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 38(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 38(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    54
  WHITE                                                       247
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED     0  53
  DEL PEAK 38(17Q24.3) WILD-TYPE   5 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED      0   53
  DEL PEAK 38(17Q24.3) WILD-TYPE    5  295
                        clus
vv                       DEL PEAK 38(17Q24.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK 38(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            295
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 39(18P11.31) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 39(18P11.31) MUTATED   290  67
  DEL PEAK 39(18P11.31) WILD-TYPE 182  54
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            357                             236 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                             67                              54 
$`DEL PEAK 39(18P11.31) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5662 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-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       37.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       14.01        33.99        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       50.04        47.01        15.02        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        25.02        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03        10.06        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       17.03        24.03        27.02        18.05        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        26.01        24.00         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        38.04        27.02        42.02        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
        1.02        15.02        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       26.01         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        15.52         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
        0.20        16.44        14.50         0.95        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 
       17.85        18.84       109.28         5.65         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        65.00        62.79        12.10        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        1.61        12.69         2.14         3.29         0.07        12.20 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
       14.30        49.08         9.99         1.91        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03         2.96        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.01        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       45.40        12.26        56.09        55.92        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 
        1.32        17.85        17.13        12.49         1.48        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04         4.80        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 
      130.65        13.32        12.59       140.38        44.32       139.17 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 
       26.47       119.93        35.97       117.07        95.18        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        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       33.67        13.25         0.53        47.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       82.39        23.51        65.85        55.04        63.62        61.91 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        91.79        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       19.33        12.79        17.85        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
        8.42        21.90        30.28        11.90        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       14.50        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-3611 TCGA-AG-3612 
       34.03        50.04         0.99        15.95        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99        29.98        37.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        36.95        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        46.03        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        15.95         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       70.03        10.98        51.98         1.94        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
       38.56         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       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-6509 
       24.13        51.48         0.49         2.40        20.55        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-F5-6465 TCGA-F5-6571 
       11.51        10.78        13.64        11.97        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
       12.46        18.28        55.76 

$`DEL PEAK 39(18P11.31) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 
        9.53        46.65        42.90        37.02        31.63        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 
       22.06        22.52         8.38        24.16        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       19.66        16.24        24.92         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
       63.98         1.02        13.02         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 
        8.05         0.00        29.00        12.99         0.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       17.95        29.95        20.98        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
        0.92        47.05        11.01         5.98         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       19.04        19.04        10.06        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       17.98        15.95         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       32.05        53.00        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3982 
       26.01        24.00         2.01         2.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       19.07        27.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
        4.01         0.99        17.03        34.98        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
        0.07        21.37        56.55         0.72        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X 
        0.92        27.09        16.31        21.44        17.82        19.33 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 
       75.95        58.39         1.41        32.94        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         3.19         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-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-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-4751 TCGA-CM-5348 TCGA-CM-5860 
       20.02        37.02        26.04        27.02        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-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 
       14.04        12.95        13.05        11.08        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       17.75        43.27        15.12         4.80        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
        3.68         4.41         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA 
       10.26       119.70        92.75        49.91         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G 
      135.65         7.76         6.12        14.04        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 
       98.24         8.61        35.74         6.18        47.87        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      133.18        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       35.80        26.17        79.69        19.33         9.93        15.65 
TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 
       29.46        31.30        70.03        19.10        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3591 
       10.39        12.00        32.02         8.02         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 
        2.01        12.03         6.05        19.99         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 
       19.04        17.95        13.02        14.01        14.04        20.98 
TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       23.01        36.03        64.01        49.97        38.96        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 
        1.45         1.81         5.29        32.61        19.96        20.91 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         8.45         9.96         0.53         1.12 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                         20.050                          19.625 
[1] "0.1 - 140.4 (20.1)" "0.0 - 148.0 (19.6)"
[1] "hr=" "1.2"
D66V2, continuous
D66V3, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   243 122
  DEL PEAK 39(18P11.31) WILD-TYPE 203  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    243  122
  DEL PEAK 39(18P11.31) WILD-TYPE  203   40
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  COLON                            243                             203
  RECTUM                           122                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18P11.31) MUTATED        57        0       14        98         4
  DEL PEAK 39(18P11.31) WILD-TYPE      47        1       22        75         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18P11.31) MUTATED           3        12         12         54
  DEL PEAK 39(18P11.31) WILD-TYPE         0        14          6         29
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(18P11.31) MUTATED           33       48        24         1
  DEL PEAK 39(18P11.31) WILD-TYPE         21       15         2         1
D66V4, multiclass
            clus
vv           DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  STAGE I                               57                              47
  STAGE IA                               0                               1
  STAGE II                              14                              22
  STAGE IIA                             98                              75
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             12                              14
  STAGE IIIA                            12                               6
  STAGE IIIB                            54                              29
  STAGE IIIC                            33                              21
  STAGE IV                              48                              15
  STAGE IVA                             24                               2
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 39(18P11.31) MUTATED    11  61 255  41
  DEL PEAK 39(18P11.31) WILD-TYPE   9  45 162  26
D66V5, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  T1                            11                               9
  T2                            61                              45
  T3                           255                             162
  T4                            41                              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 39(18P11.31) MUTATED   190 104  73
  DEL PEAK 39(18P11.31) WILD-TYPE 155  46  42
D66V6, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  N0                           190                             155
  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"
D66V7, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   256  72
  DEL PEAK 39(18P11.31) WILD-TYPE 194  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    256   72
  DEL PEAK 39(18P11.31) WILD-TYPE  194   16
   clus
vv  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  0                           256                             194
  1                            72                              16
[1] 2 2
[1] FALSE
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   169 199
  DEL PEAK 39(18P11.31) WILD-TYPE 118 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    169  199
  DEL PEAK 39(18P11.31) WILD-TYPE  118  126
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  FEMALE                           169                             118
  MALE                             199                             126
[1] 2 2
[1] FALSE
D66V9, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   270  18
  DEL PEAK 39(18P11.31) WILD-TYPE 176  10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    270   18
  DEL PEAK 39(18P11.31) WILD-TYPE  176   10
     clus
vv    DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  NO                            270                             176
  YES                            18                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                    231
  DEL PEAK 39(18P11.31) WILD-TYPE                  151
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                               9
  DEL PEAK 39(18P11.31) WILD-TYPE                            51
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                     116
  DEL PEAK 39(18P11.31) WILD-TYPE                    30
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                                6
  DEL PEAK 39(18P11.31) WILD-TYPE                              7
D66V10, multiclass
                                clus
vv                               DEL PEAK 39(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                     231
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                    116
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 39(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       151
  COLON MUCINOUS ADENOCARCINOMA                               51
  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 39(18P11.31) MUTATED   263   2  29  14
  DEL PEAK 39(18P11.31) WILD-TYPE 179   3   8  15
D66V11, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  R0                           263                             179
  R1                             2                               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"
D66V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(18P11.31) MUTATED                                  1     6
  DEL PEAK 39(18P11.31) WILD-TYPE                                0     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(18P11.31) MUTATED                          41   180
  DEL PEAK 39(18P11.31) WILD-TYPE                        23   112
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 39(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      180
                                  clus
vv                                 DEL PEAK 39(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED     4 212
  DEL PEAK 39(18P11.31) WILD-TYPE   1 136
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED      4  212
  DEL PEAK 39(18P11.31) WILD-TYPE    1  136
                        clus
vv                       DEL PEAK 39(18P11.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           212
                        clus
vv                       DEL PEAK 39(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             136
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 40(18Q12.2) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(18Q12.2) MUTATED   324  78
  DEL PEAK 40(18Q12.2) WILD-TYPE 148  43
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           402                            191 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                            78                             43 
$`DEL PEAK 40(18Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 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-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       22.52        24.13        25.18        20.61        21.76        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-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03        19.07        19.07        34.03 
TCGA-AA-3532 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-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        25.02        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03        10.06        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        19.00        34.03        18.05        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99         1.02        15.02        10.98        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       15.52         0.79         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
        0.20        16.44         0.46        14.50        16.31        33.01 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4681 
       17.26        17.85        18.84       109.28         5.13       106.75 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        88.21        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        5.23         1.61        12.69         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       12.20        14.30       148.01        49.08         9.99         1.91 
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-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       16.04        21.99        13.02        15.02        11.01        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        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.19        18.25         1.32 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85        17.13        12.49        15.58         1.48         4.41 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       12.43        14.30         9.04         4.80        11.38        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-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       14.04        26.47       119.93       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       31.96        11.11        35.74         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       16.24        13.25         0.53        47.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       39.42        35.93        61.91        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 
       74.79        18.18        10.98        19.33        12.79        17.85 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       16.80        42.77        32.98         8.42        21.90        30.28 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       19.10        34.49        37.74        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        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-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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        6.05         0.99        15.95        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72        26.43        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 40(18Q12.2) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
        9.53        46.65        42.90        33.53        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        24.16        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       19.66        16.24        24.92         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3529 
       63.98         1.02        13.02         1.02         8.05         0.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
       29.00         0.99        17.95        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
       54.02         0.92        47.05        11.01         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       19.04        19.04        10.06        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       17.98        15.95         0.00         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-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       24.00         2.01        25.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        38.04         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-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y 
       35.01        35.01        39.06        51.98        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AM-5821 
       18.05         0.07        21.37        56.55         0.72         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 
       27.09         0.95        21.44        17.82        19.33        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39         1.41         5.65        32.94        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
      100.01        11.74         3.19         3.06         3.25        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-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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        14.99        12.99        14.04        12.95        13.05 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        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 
        3.68         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      119.70       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        35.74         6.18        47.87        33.67        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      133.18        74.56        67.30        53.62        85.48        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        79.69 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       19.33         9.93        15.65        29.46        31.30        70.03 
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
       16.83         8.02         1.02        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A025 
       13.02        14.01        20.98        36.03         9.07        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                         19.99                          19.99 
[1] "0.1 - 148.0 (20.0)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   271 139
  DEL PEAK 40(18Q12.2) WILD-TYPE 175  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    271  139
  DEL PEAK 40(18Q12.2) WILD-TYPE  175   23
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON                           271                            175
  RECTUM                          139                             23
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18Q12.2) MUTATED        60        0       21       107         4
  DEL PEAK 40(18Q12.2) WILD-TYPE      44        1       15        66         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q12.2) MUTATED           3        16         15         61
  DEL PEAK 40(18Q12.2) WILD-TYPE         0        10          3         22
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18Q12.2) MUTATED           39       53        23         1
  DEL PEAK 40(18Q12.2) WILD-TYPE         15       10         3         1
D67V4, multiclass
            clus
vv           DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  STAGE I                              60                             44
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                           107                             66
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           15                              3
  STAGE IIIB                           61                             22
  STAGE IIIC                           39                             15
  STAGE IV                             53                             10
  STAGE IVA                            23                              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 40(18Q12.2) MUTATED    11  67 291  43
  DEL PEAK 40(18Q12.2) WILD-TYPE   9  39 126  24
D67V5, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  T1                           11                              9
  T2                           67                             39
  T3                          291                            126
  T4                           43                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 40(18Q12.2) MUTATED   208 116  87
  DEL PEAK 40(18Q12.2) WILD-TYPE 137  34  28
D67V6, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  N0                          208                            137
  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"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   294  74
  DEL PEAK 40(18Q12.2) WILD-TYPE 156  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    294   74
  DEL PEAK 40(18Q12.2) WILD-TYPE  156   14
   clus
vv  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  0                          294                            156
  1                           74                             14
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   186 227
  DEL PEAK 40(18Q12.2) WILD-TYPE 101  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    186  227
  DEL PEAK 40(18Q12.2) WILD-TYPE  101   98
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  FEMALE                          186                            101
  MALE                            227                             98
[1] 2 2
[1] FALSE
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   296  24
  DEL PEAK 40(18Q12.2) WILD-TYPE 150   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    296   24
  DEL PEAK 40(18Q12.2) WILD-TYPE  150    4
     clus
vv    DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  NO                           296                            150
  YES                           24                              4
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                    254
  DEL PEAK 40(18Q12.2) WILD-TYPE                  128
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                              14
  DEL PEAK 40(18Q12.2) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                     128
  DEL PEAK 40(18Q12.2) WILD-TYPE                    18
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                               10
  DEL PEAK 40(18Q12.2) WILD-TYPE                              3
D67V10, multiclass
                                clus
vv                               DEL PEAK 40(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    254
  COLON MUCINOUS ADENOCARCINOMA                            14
  RECTAL ADENOCARCINOMA                                   128
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  COLON MUCINOUS ADENOCARCINOMA                              46
  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 40(18Q12.2) MUTATED   296   3  29  14
  DEL PEAK 40(18Q12.2) WILD-TYPE 146   2   8  15
D67V11, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  R0                          296                            146
  R1                            3                              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"
D67V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(18Q12.2) MUTATED                                  1     6
  DEL PEAK 40(18Q12.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18Q12.2) MUTATED                          41   203
  DEL PEAK 40(18Q12.2) WILD-TYPE                        23    89
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  41
  WHITE                                                     203
                                  clus
vv                                 DEL PEAK 40(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                        89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED     4 235
  DEL PEAK 40(18Q12.2) WILD-TYPE   1 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED      4  235
  DEL PEAK 40(18Q12.2) WILD-TYPE    1  113
                        clus
vv                       DEL PEAK 40(18Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          235
                        clus
vv                       DEL PEAK 40(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            113
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 41(18Q21.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q21.2) MUTATED   337  82
  DEL PEAK 41(18Q21.2) WILD-TYPE 135  39
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           419                            174 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                            82                             39 
$`DEL PEAK 41(18Q21.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 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-3496 TCGA-AA-3511 
        5.03         7.04         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        34.03        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       18.05        42.02        17.03        14.99        21.99         1.02 
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-6888 TCGA-AD-6890 TCGA-AD-6899 
        0.92        41.00        40.96        15.52         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42         0.20        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       16.31        33.01        17.82        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28         5.65         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       12.20        14.30       148.01        49.08         9.99         1.91 
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-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03         2.96        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       16.04        21.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       12.26        19.59        56.09        55.92        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25         1.32        17.85        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        1.48         4.41        12.43        14.30         9.04         4.80 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       13.25         0.53        47.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 
       39.42        35.93        61.91        36.00        26.04        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       46.75        74.79        18.18        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        17.85        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        30.28        11.90        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        15.39        20.02        10.39        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-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04         6.05         0.99        15.95 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        17.03        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-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        46.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04        38.56         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        10.19         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         8.45        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 41(18Q21.2) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
        9.53        46.65        42.90        33.53        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.08        24.16        24.69        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       24.92         3.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3543 
       13.02         1.02         8.05         0.00        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 
       17.95        29.95        20.98         6.97         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       11.01         5.03        26.99        19.04        19.04        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-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       38.04         4.01        27.02         0.99        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       31.00        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       51.98        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.72        10.88         0.92        27.09         0.95 
TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       21.44        19.33        75.95        58.39         1.41        32.94 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       49.41         6.77       100.01         3.06         3.25        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-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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6530 
       12.00        14.99        12.99        14.04        12.95        20.42 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       43.27        15.12         4.80        16.14         3.68         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64         1.51        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       35.31       133.18        67.30        53.62        85.48        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       22.09        13.78        35.80        26.17        79.69        19.33 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3580 
       15.65        29.46        31.30        70.03        16.83         8.02 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       12.03        19.99         0.99        13.02        14.01        20.98 
TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DY-A1H8 
       36.03        49.97        61.97         1.45         1.81        32.61 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       19.96         8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        19.990                         20.005 
[1] "0.1 - 148.0 (20.0)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.1"
D68V2, continuous
D68V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   285 142
  DEL PEAK 41(18Q21.2) WILD-TYPE 161  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    285  142
  DEL PEAK 41(18Q21.2) WILD-TYPE  161   20
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON                           285                            161
  RECTUM                          142                             20
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(18Q21.2) MUTATED        62        0       23       109         4
  DEL PEAK 41(18Q21.2) WILD-TYPE      42        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q21.2) MUTATED           3        17         15         64
  DEL PEAK 41(18Q21.2) WILD-TYPE         0         9          3         19
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(18Q21.2) MUTATED           42       56        24         2
  DEL PEAK 41(18Q21.2) WILD-TYPE         12        7         2         0
D68V4, multiclass
            clus
vv           DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           109                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            17                              9
  STAGE IIIA                           15                              3
  STAGE IIIB                           64                             19
  STAGE IIIC                           42                             12
  STAGE IV                             56                              7
  STAGE IVA                            24                              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 41(18Q21.2) MUTATED    12  68 302  47
  DEL PEAK 41(18Q21.2) WILD-TYPE   8  38 115  20
D68V5, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  T1                           12                              8
  T2                           68                             38
  T3                          302                            115
  T4                           47                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 41(18Q21.2) MUTATED   214 120  94
  DEL PEAK 41(18Q21.2) WILD-TYPE 131  30  21
D68V6, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  N0                          214                            131
  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"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   304  79
  DEL PEAK 41(18Q21.2) WILD-TYPE 146   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    304   79
  DEL PEAK 41(18Q21.2) WILD-TYPE  146    9
   clus
vv  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  0                          304                            146
  1                           79                              9
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   191 239
  DEL PEAK 41(18Q21.2) WILD-TYPE  96  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    191  239
  DEL PEAK 41(18Q21.2) WILD-TYPE   96   86
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  FEMALE                          191                             96
  MALE                            239                             86
[1] 2 2
[1] FALSE
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   310  24
  DEL PEAK 41(18Q21.2) WILD-TYPE 136   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    310   24
  DEL PEAK 41(18Q21.2) WILD-TYPE  136    4
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  NO                           310                            136
  YES                           24                              4
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                    266
  DEL PEAK 41(18Q21.2) WILD-TYPE                  116
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                              16
  DEL PEAK 41(18Q21.2) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                     129
  DEL PEAK 41(18Q21.2) WILD-TYPE                    17
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                               11
  DEL PEAK 41(18Q21.2) WILD-TYPE                              2
D68V10, multiclass
                                clus
vv                               DEL PEAK 41(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                    266
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                   129
  RECTAL MUCINOUS ADENOCARCINOMA                           11
                                clus
vv                               DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      116
  COLON MUCINOUS ADENOCARCINOMA                              44
  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 41(18Q21.2) MUTATED   306   3  30  15
  DEL PEAK 41(18Q21.2) WILD-TYPE 136   2   7  14
D68V11, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  R0                          306                            136
  R1                            3                              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"
D68V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(18Q21.2) MUTATED                                  1     7
  DEL PEAK 41(18Q21.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q21.2) MUTATED                          45   212
  DEL PEAK 41(18Q21.2) WILD-TYPE                        19    80
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  45
  WHITE                                                     212
                                  clus
vv                                 DEL PEAK 41(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                        80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED     4 249
  DEL PEAK 41(18Q21.2) WILD-TYPE   1  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED      4  249
  DEL PEAK 41(18Q21.2) WILD-TYPE    1   99
                        clus
vv                       DEL PEAK 41(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          249
                        clus
vv                       DEL PEAK 41(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             99
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 42(18Q22.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q22.1) MUTATED   333  82
  DEL PEAK 42(18Q22.1) WILD-TYPE 139  39
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           415                            178 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                            82                             39 
$`DEL PEAK 42(18Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 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-3496 TCGA-AA-3511 
        5.03         7.04         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        34.03        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 
       27.02        29.98        18.05        12.99        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       34.06        26.01        24.00        27.02         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       19.00        34.03        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S 
        1.02        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-6888 TCGA-AD-6890 
        5.03         0.92        41.00        40.96        15.52         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42         0.20        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31        33.01        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28         5.65         5.13       106.75        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        88.21        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.61        12.69         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
       12.20        14.30        49.08         9.99         1.91        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.03        30.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03         2.96        29.03        16.04 
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-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        12.26 
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-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
        1.32        15.12        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 
        1.48         4.41        12.43        14.30         9.04         4.80 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        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        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       13.25         0.53        47.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        65.85        44.68        55.04        63.62 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       39.42        35.93        61.91        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC 
       74.79        18.18        10.98        19.33         9.93        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       17.85        16.80        42.77        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        11.90        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        34.49        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        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-3611 TCGA-AG-3612 
       50.04         6.05         0.99        15.95        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
       38.56         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       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         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-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        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 42(18Q22.1) WILD-TYPE`
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 
        9.53        46.65        42.90        33.53        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.08        24.16        24.69        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       24.92         3.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3543 
       13.02         1.02         8.05         0.00        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 
       17.95        29.95        20.98         6.97         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       11.01         5.03        26.99        19.04        19.04        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-3877 TCGA-AA-3930 
        0.00         0.00        36.03        32.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 
       33.01        26.01        24.00         2.01        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       27.02        38.04        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       38.07         1.02        35.01        35.01        39.06        51.98 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 
        0.72        10.88         0.92        27.09         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.82        19.33        75.95        58.39         1.41        32.94 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       49.41         6.77       100.01         3.06         3.25        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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       20.42        43.27         4.80        16.14         3.68         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64         1.51        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       35.31       133.18        67.30        53.62        85.48        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        79.69 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 
       19.33        15.65        29.46        31.30        70.03        16.83 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 
        8.02         1.02        12.03        19.99        37.02         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N 
       13.02        14.01        20.98        36.03        49.97        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 
        1.45         1.81         5.29        32.61        19.96         8.61 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       17.46         9.96         0.53         1.12 

  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                        19.990                         20.005 
[1] "0.1 - 140.4 (20.0)" "0.0 - 148.0 (20.0)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   284 138
  DEL PEAK 42(18Q22.1) WILD-TYPE 162  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    284  138
  DEL PEAK 42(18Q22.1) WILD-TYPE  162   24
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON                           284                            162
  RECTUM                          138                             24
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(18Q22.1) MUTATED        62        0       23       109         4
  DEL PEAK 42(18Q22.1) WILD-TYPE      42        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q22.1) MUTATED           3        14         15         63
  DEL PEAK 42(18Q22.1) WILD-TYPE         0        12          3         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(18Q22.1) MUTATED           42       55        24         2
  DEL PEAK 42(18Q22.1) WILD-TYPE         12        8         2         0
D69V4, multiclass
            clus
vv           DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           109                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            14                             12
  STAGE IIIA                           15                              3
  STAGE IIIB                           63                             20
  STAGE IIIC                           42                             12
  STAGE IV                             55                              8
  STAGE IVA                            24                              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(18Q22.1) MUTATED    12  68 297  47
  DEL PEAK 42(18Q22.1) WILD-TYPE   8  38 120  20
D69V5, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  T1                           12                              8
  T2                           68                             38
  T3                          297                            120
  T4                           47                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 42(18Q22.1) MUTATED   214 116  93
  DEL PEAK 42(18Q22.1) WILD-TYPE 131  34  22
D69V6, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  N0                          214                            131
  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"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   301  78
  DEL PEAK 42(18Q22.1) WILD-TYPE 149  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    301   78
  DEL PEAK 42(18Q22.1) WILD-TYPE  149   10
   clus
vv  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  0                          301                            149
  1                           78                             10
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   189 236
  DEL PEAK 42(18Q22.1) WILD-TYPE  98  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    189  236
  DEL PEAK 42(18Q22.1) WILD-TYPE   98   89
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  FEMALE                          189                             98
  MALE                            236                             89
[1] 2 2
[1] FALSE
D69V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   308  24
  DEL PEAK 42(18Q22.1) WILD-TYPE 138   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    308   24
  DEL PEAK 42(18Q22.1) WILD-TYPE  138    4
     clus
vv    DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  NO                           308                            138
  YES                           24                              4
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                    266
  DEL PEAK 42(18Q22.1) WILD-TYPE                  116
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                              15
  DEL PEAK 42(18Q22.1) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                     127
  DEL PEAK 42(18Q22.1) WILD-TYPE                    19
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                               10
  DEL PEAK 42(18Q22.1) WILD-TYPE                              3
D69V10, multiclass
                                clus
vv                               DEL PEAK 42(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    266
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                   127
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      116
  COLON MUCINOUS ADENOCARCINOMA                              45
  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 42(18Q22.1) MUTATED   303   3  29  15
  DEL PEAK 42(18Q22.1) WILD-TYPE 139   2   8  14
D69V11, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  R0                          303                            139
  R1                            3                              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"
D69V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(18Q22.1) MUTATED                                  1     6
  DEL PEAK 42(18Q22.1) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q22.1) MUTATED                          44   210
  DEL PEAK 42(18Q22.1) WILD-TYPE                        20    82
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  44
  WHITE                                                     210
                                  clus
vv                                 DEL PEAK 42(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                        82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED     4 245
  DEL PEAK 42(18Q22.1) WILD-TYPE   1 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED      4  245
  DEL PEAK 42(18Q22.1) WILD-TYPE    1  103
                        clus
vv                       DEL PEAK 42(18Q22.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          245
                        clus
vv                       DEL PEAK 42(18Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            103
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 43(19P13.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(19P13.3) MUTATED    69  23
  DEL PEAK 43(19P13.3) WILD-TYPE 403  98
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            92                            501 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            23                             98 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-4N-A93T TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3506 
        4.80        34.65        25.08        21.76        61.84        58.03 
TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 
        9.07        26.01        12.99        13.02        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3850 
        6.05         2.01        36.00        36.95        37.02         0.00 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3952 
       31.07        17.03        24.03        27.02        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T 
       50.99        24.00        27.02        10.98        12.00        33.04 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 
       26.01        39.98        41.00        22.42         0.20        16.31 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6169 
        5.13        65.00         3.29       148.01        49.08        13.02 
TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 
       13.05        10.06        45.40        20.19         1.32         4.80 
TCGA-D5-6541 TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-F4-6461 
       15.58         4.41       119.70        44.32       131.51        11.11 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL 
       33.67         8.35        82.39        36.00        10.98        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 
       24.13        39.48        14.50        12.00        36.03        15.95 
TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-4008 
       13.94        20.98        32.98        19.04        35.01        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-4957 
       15.95         9.07        64.01         6.05        33.17        12.39 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03        13.97        10.98         5.29       129.27        24.13 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 TCGA-F5-6702 
       51.48        17.00        16.34        13.64        31.30        28.57 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`DEL PEAK 43(19P13.3) WILD-TYPE`
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-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-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-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00         5.03        85.05        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        14.93         0.00        17.03        10.06 
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-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       53.00        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98         1.02        15.02        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       15.52        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88        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-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84       109.28        75.95        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94       106.75        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.61        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07        12.20        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         9.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         1.91       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-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-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 
        2.96        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.03        12.26        19.59        56.09        55.92 
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-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14         1.48         3.68        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64         4.80         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        31.96        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        47.41        35.31       133.18        28.21        23.51 
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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       85.48        63.62        39.42        35.93        61.91        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        79.69        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        15.65        12.79        17.85        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        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 
       86.63        65.98        11.84        36.03        32.02         8.02 
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-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-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        36.03         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81        10.19         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        8.98        15.02        27.95        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
        5.03       126.44        41.36        57.24        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        49.51        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                        20.585                         19.990 
[1] "0.0 - 148.0 (20.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D70V2, continuous
D70V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    62  33
  DEL PEAK 43(19P13.3) WILD-TYPE 384 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     62   33
  DEL PEAK 43(19P13.3) WILD-TYPE  384  129
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  COLON                            62                            384
  RECTUM                           33                            129
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(19P13.3) MUTATED        11        0        4        19         0
  DEL PEAK 43(19P13.3) WILD-TYPE      93        1       32       154        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(19P13.3) MUTATED           1         6          4         10
  DEL PEAK 43(19P13.3) WILD-TYPE         2        20         14         73
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(19P13.3) MUTATED           15       15         8         1
  DEL PEAK 43(19P13.3) WILD-TYPE         39       48        18         1
D70V4, multiclass
            clus
vv           DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                              11                             93
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            19                            154
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            4                             14
  STAGE IIIB                           10                             73
  STAGE IIIC                           15                             39
  STAGE IV                             15                             48
  STAGE IVA                             8                             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 43(19P13.3) MUTATED     1  13  71  11
  DEL PEAK 43(19P13.3) WILD-TYPE  19  93 346  56
D70V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T1                            1                             19
  T2                           13                             93
  T3                           71                            346
  T4                           11                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 43(19P13.3) MUTATED    36  28  32
  DEL PEAK 43(19P13.3) WILD-TYPE 309 122  83
D70V6, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           36                            309
  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"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    63  23
  DEL PEAK 43(19P13.3) WILD-TYPE 387  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     63   23
  DEL PEAK 43(19P13.3) WILD-TYPE  387   65
   clus
vv  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  0                           63                            387
  1                           23                             65
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    40  56
  DEL PEAK 43(19P13.3) WILD-TYPE 247 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     40   56
  DEL PEAK 43(19P13.3) WILD-TYPE  247  269
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           40                            247
  MALE                             56                            269
[1] 2 2
[1] FALSE
D70V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    73   2
  DEL PEAK 43(19P13.3) WILD-TYPE 373  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     73    2
  DEL PEAK 43(19P13.3) WILD-TYPE  373   26
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                            73                            373
  YES                            2                             26
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                     56
  DEL PEAK 43(19P13.3) WILD-TYPE                  326
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                               5
  DEL PEAK 43(19P13.3) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                      31
  DEL PEAK 43(19P13.3) WILD-TYPE                   115
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                1
  DEL PEAK 43(19P13.3) WILD-TYPE                             12
D70V10, multiclass
                                clus
vv                               DEL PEAK 43(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                     56
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 43(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      326
  COLON MUCINOUS ADENOCARCINOMA                              55
  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 43(19P13.3) MUTATED    63   1  10   4
  DEL PEAK 43(19P13.3) WILD-TYPE 379   4  27  25
D70V11, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  R0                           63                            379
  R1                            1                              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"
D70V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(19P13.3) MUTATED                                  0     2
  DEL PEAK 43(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(19P13.3) MUTATED                           8    42
  DEL PEAK 43(19P13.3) WILD-TYPE                        56   250
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    56
  WHITE                                                       250
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED     1  49
  DEL PEAK 43(19P13.3) WILD-TYPE   4 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED      1   49
  DEL PEAK 43(19P13.3) WILD-TYPE    4  299
                        clus
vv                       DEL PEAK 43(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           49
                        clus
vv                       DEL PEAK 43(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            299
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 44(20P12.1) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(20P12.1) MUTATED   102  28
  DEL PEAK 44(20P12.1) WILD-TYPE 370  93
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           130                            463 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                            28                             93 
$`DEL PEAK 44(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       24.33        14.53        29.19        23.61        32.71        29.16 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3519 
       24.13        25.18        21.76         1.02        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3561 
       34.03        26.01        12.99         0.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3855 
       78.08         5.98        85.05        25.02        36.95        32.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
       24.03         2.01        20.98         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F 
       42.02        32.02        31.00         1.02        37.02        39.98 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 
       40.96         0.20        33.01       109.28        62.79         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 
       11.74         1.61       148.01         9.99         1.91        22.03 
TCGA-CM-5349 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       30.08        29.03        12.99        13.02        15.02        11.08 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6929 TCGA-D5-6932 
       56.09        55.92         1.32        43.27         4.80        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28E TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      131.51        26.47       119.93        41.42        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 TCGA-G4-6320 
       13.25         0.53         8.35        23.51        61.91        26.43 
TCGA-NH-A50V TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2689 
       19.33        16.80         8.42        30.28        11.90        39.48 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       10.39        14.50        86.63        65.98        11.84        36.03 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3600 TCGA-AG-3608 
       32.02         7.07        20.05        24.00         6.05        15.95 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J 
        0.99         1.02        32.02        46.03        13.94         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       12.00        31.00        70.03        64.01         1.94        38.96 
TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6624 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
        1.45         0.69         4.73         8.98        10.98        19.99 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 
        5.03        41.36        57.24        24.13        32.61         2.40 
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 TCGA-G5-6641 
       31.30        28.57        12.46        26.43 

$`DEL PEAK 44(20P12.1) WILD-TYPE`
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        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-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       31.63        30.44        33.53        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       22.52         8.38        25.08        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-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-3506 TCGA-AA-3510 
        3.02         1.02        37.05        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 
       36.03         8.05        19.07         0.00        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
       29.00        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
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-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         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-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       24.00        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98         1.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        26.01        39.06        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-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37        15.52        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.92        14.50        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 
       17.82        17.26        17.85        19.33        18.84        75.95 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13       106.75 
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-6601 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
      100.01        29.56         3.19        12.69         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       14.30        17.56        85.45        70.16        15.62        49.08 
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-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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.98        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-6165 
       15.02        17.03        15.02        12.00         2.96        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       21.99        14.99        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        12.26 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 
       19.59        20.19        20.42        17.75        18.25        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 
        1.48         3.68         4.41        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         1.51        12.00        10.26        24.43 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        14.04        81.37        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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18        28.21        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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       63.62        39.42        35.93        36.00        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        74.79 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       79.69        18.18        10.98        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       12.79        17.85        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       21.90        70.03        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        34.49        37.74        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
       10.39        12.00         8.02        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        19.99        13.94        19.99        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-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         3.98        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
       38.56         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       33.17         6.97         9.37        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       21.01        11.01        15.02         5.03        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       27.95         5.95         4.01         5.29       126.44       129.27 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       18.28        16.34        16.31         8.61        13.64        17.46 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97         9.96        49.51         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                         23.56                          19.96 
[1] "0.2 - 148.0 (23.6)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    84  48
  DEL PEAK 44(20P12.1) WILD-TYPE 362 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     84   48
  DEL PEAK 44(20P12.1) WILD-TYPE  362  114
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  COLON                            84                            362
  RECTUM                           48                            114
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 44(20P12.1) MUTATED        17        0       11        32         0
  DEL PEAK 44(20P12.1) WILD-TYPE      87        1       25       141        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(20P12.1) MUTATED           2         5          5         22
  DEL PEAK 44(20P12.1) WILD-TYPE         1        21         13         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(20P12.1) MUTATED           15       14         8         0
  DEL PEAK 44(20P12.1) WILD-TYPE         39       49        18         2
D71V4, multiclass
            clus
vv           DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  STAGE I                              17                             87
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            32                            141
  STAGE IIB                             0                             10
  STAGE IIC                             2                              1
  STAGE III                             5                             21
  STAGE IIIA                            5                             13
  STAGE IIIB                           22                             61
  STAGE IIIC                           15                             39
  STAGE IV                             14                             49
  STAGE IVA                             8                             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 44(20P12.1) MUTATED     3  20  96  14
  DEL PEAK 44(20P12.1) WILD-TYPE  17  86 321  53
D71V5, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  T1                            3                             17
  T2                           20                             86
  T3                           96                            321
  T4                           14                             53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 44(20P12.1) MUTATED    67  36  30
  DEL PEAK 44(20P12.1) WILD-TYPE 278 114  85
D71V6, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  N0                           67                            278
  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"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED   101  20
  DEL PEAK 44(20P12.1) WILD-TYPE 349  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED    101   20
  DEL PEAK 44(20P12.1) WILD-TYPE  349   68
   clus
vv  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  0                          101                            349
  1                           20                             68
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    65  68
  DEL PEAK 44(20P12.1) WILD-TYPE 222 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     65   68
  DEL PEAK 44(20P12.1) WILD-TYPE  222  257
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  FEMALE                           65                            222
  MALE                             68                            257
[1] 2 2
[1] FALSE
D71V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    91   4
  DEL PEAK 44(20P12.1) WILD-TYPE 355  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     91    4
  DEL PEAK 44(20P12.1) WILD-TYPE  355   24
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  NO                            91                            355
  YES                            4                             24
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                     77
  DEL PEAK 44(20P12.1) WILD-TYPE                  305
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                               5
  DEL PEAK 44(20P12.1) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                      43
  DEL PEAK 44(20P12.1) WILD-TYPE                   103
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                                5
  DEL PEAK 44(20P12.1) WILD-TYPE                              8
D71V10, multiclass
                                clus
vv                               DEL PEAK 44(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                     77
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 44(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      305
  COLON MUCINOUS ADENOCARCINOMA                              55
  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 44(20P12.1) MUTATED    92   1   8   3
  DEL PEAK 44(20P12.1) WILD-TYPE 350   4  29  26
D71V11, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  R0                           92                            350
  R1                            1                              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"
D71V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(20P12.1) MUTATED                                  0     0
  DEL PEAK 44(20P12.1) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(20P12.1) MUTATED                          14    69
  DEL PEAK 44(20P12.1) WILD-TYPE                        50   223
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 44(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      69
                                  clus
vv                                 DEL PEAK 44(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED     1  78
  DEL PEAK 44(20P12.1) WILD-TYPE   4 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED      1   78
  DEL PEAK 44(20P12.1) WILD-TYPE    4  270
                        clus
vv                       DEL PEAK 44(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           78
                        clus
vv                       DEL PEAK 44(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 45(21Q11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q11.2) MUTATED   162  43
  DEL PEAK 45(21Q11.2) WILD-TYPE 310  78
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           205                            388 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                            43                             78 
$`DEL PEAK 45(21Q11.2) MUTATED`
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 
        1.61        39.45        43.76        43.76        42.28        37.05 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 
       14.53        30.44        22.09        22.06        29.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       21.76        24.39        23.87        20.28        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3530 
        5.03         6.97        38.99         9.07        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       34.03        26.01        14.01        13.02        23.01        19.99 
TCGA-AA-3660 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3837 
       78.08        37.05        19.00        36.00        10.06        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       37.02        14.93        10.06         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 
       24.03        27.02        18.05        24.00        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       21.99         7.96        13.94        38.04        27.02        42.02 
TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 
       21.99        15.02        10.98        32.02        31.00        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 
       39.98         2.01         0.92        41.00         0.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D 
        0.20        16.44        14.50        16.31         0.95        17.85 
TCGA-AY-A71X TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       19.33         5.13        65.00        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 
        3.19        12.69         2.14         3.29        12.20        49.08 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
        9.99         1.91        20.02         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 
       22.03        32.02         5.03        15.02         2.96        29.03 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 
       15.02        11.08        11.01        45.40        17.75         1.32 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        4.41        12.43        14.30         9.04         4.80        11.38 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A 
       49.91        13.32       140.38         7.50       131.51        26.47 
TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       31.96        47.87         1.55        41.42        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
        0.53        47.41         8.35        35.93        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A8F7 
       26.43        91.79        46.75        18.18         9.93        17.85 
TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 
       42.77        24.13        39.48        17.23        19.10        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        10.39        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-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       19.99        17.03         1.02        48.03        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       14.04        17.03        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       10.98         1.94        38.96        61.97        41.00        38.56 
TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 
        0.69         4.73        12.39        21.01        13.97        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG 
       10.98         4.01         5.03       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         0.49         2.40        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        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 
        0.39        32.19         0.66         0.53         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 45(21Q11.2) WILD-TYPE`
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-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       16.57        37.25        37.02        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 
       32.91        31.63        29.19        33.53        23.61        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-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       56.25         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3532 
       24.03        37.05        36.03         8.05         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        12.99         0.99        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       17.95        29.95        20.98        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        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-3870 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       12.99        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98         1.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R 
       26.01        37.02        39.06         2.96         5.03        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.72         5.79        27.42        10.88         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-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84       109.28        75.95        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94       106.75        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         1.61         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07        12.76        10.06        14.30        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-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 
      124.27        23.05        37.02        25.02        26.04        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        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-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25        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         1.48         3.68 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A285 TCGA-DM-A288 TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        35.74        35.74         6.18        34.42 
TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       13.25        35.31       133.18        28.21        82.39        23.51 
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-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       85.48        63.62        39.42        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       35.80        26.17        74.79        79.69        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        30.28        11.90        70.03 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        34.49        37.74        10.39        16.83 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 
       65.98        32.02         8.02        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
        2.01        50.04         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         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-3902 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       14.01        32.02        28.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07         1.02        51.98        49.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         1.45         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         9.37        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       11.01        15.02         5.03         8.98        15.02        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6507 
        5.95         5.29        41.36       129.27        24.13        19.96 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.00        18.28        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 
       13.64        17.46         9.96        49.51        28.57         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12        12.46        55.76        47.08 

  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                          19.1                           20.7 
[1] "0.2 - 140.4 (19.1)" "0.0 - 148.0 (20.7)"
[1] "hr=" "1.2"
D72V2, continuous
D72V3, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   138  71
  DEL PEAK 45(21Q11.2) WILD-TYPE 308  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    138   71
  DEL PEAK 45(21Q11.2) WILD-TYPE  308   91
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON                           138                            308
  RECTUM                           71                             91
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 45(21Q11.2) MUTATED        34        0       14        54         2
  DEL PEAK 45(21Q11.2) WILD-TYPE      70        1       22       119         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(21Q11.2) MUTATED           1         7         10         28
  DEL PEAK 45(21Q11.2) WILD-TYPE         2        19          8         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 45(21Q11.2) MUTATED           21       29         7         0
  DEL PEAK 45(21Q11.2) WILD-TYPE         33       34        19         2
D72V4, multiclass
            clus
vv           DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  STAGE I                              34                             70
  STAGE IA                              0                              1
  STAGE II                             14                             22
  STAGE IIA                            54                            119
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                           10                              8
  STAGE IIIB                           28                             55
  STAGE IIIC                           21                             33
  STAGE IV                             29                             34
  STAGE IVA                             7                             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 45(21Q11.2) MUTATED     7  40 142  23
  DEL PEAK 45(21Q11.2) WILD-TYPE  13  66 275  44
D72V5, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  T1                            7                             13
  T2                           40                             66
  T3                          142                            275
  T4                           23                             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 45(21Q11.2) MUTATED   108  56  48
  DEL PEAK 45(21Q11.2) WILD-TYPE 237  94  67
D72V6, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  N0                          108                            237
  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"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   151  34
  DEL PEAK 45(21Q11.2) WILD-TYPE 299  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    151   34
  DEL PEAK 45(21Q11.2) WILD-TYPE  299   54
   clus
vv  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  0                          151                            299
  1                           34                             54
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    96 116
  DEL PEAK 45(21Q11.2) WILD-TYPE 191 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     96  116
  DEL PEAK 45(21Q11.2) WILD-TYPE  191  209
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  FEMALE                           96                            191
  MALE                            116                            209
[1] 2 2
[1] FALSE
D72V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   151  12
  DEL PEAK 45(21Q11.2) WILD-TYPE 295  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    151   12
  DEL PEAK 45(21Q11.2) WILD-TYPE  295   16
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  NO                           151                            295
  YES                           12                             16
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                    128
  DEL PEAK 45(21Q11.2) WILD-TYPE                  254
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                               8
  DEL PEAK 45(21Q11.2) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                      66
  DEL PEAK 45(21Q11.2) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                3
  DEL PEAK 45(21Q11.2) WILD-TYPE                             10
D72V10, multiclass
                                clus
vv                               DEL PEAK 45(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    128
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      254
  COLON MUCINOUS ADENOCARCINOMA                              52
  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 45(21Q11.2) MUTATED   151   2  14   7
  DEL PEAK 45(21Q11.2) WILD-TYPE 291   3  23  22
D72V11, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  R0                          151                            291
  R1                            2                              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"
D72V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(21Q11.2) MUTATED                                  1     4
  DEL PEAK 45(21Q11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(21Q11.2) MUTATED                          20   105
  DEL PEAK 45(21Q11.2) WILD-TYPE                        44   187
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     105
                                  clus
vv                                 DEL PEAK 45(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED     4 120
  DEL PEAK 45(21Q11.2) WILD-TYPE   1 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED      4  120
  DEL PEAK 45(21Q11.2) WILD-TYPE    1  228
                        clus
vv                       DEL PEAK 45(21Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 45(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            228
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 46(22Q13.32) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(22Q13.32) MUTATED   169  50
  DEL PEAK 46(22Q13.32) WILD-TYPE 303  71
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            219                             374 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                             50                              71 
$`DEL PEAK 46(22Q13.32) MUTATED`
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       35.11        45.60        13.94        16.57        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       14.53        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-3520 TCGA-AA-3522 TCGA-AA-3532 
        6.97        38.99         9.07        24.03        37.05        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 
       26.01        12.99        33.99        21.01        13.02        19.99 
TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3681 TCGA-AA-3685 
       13.94         6.05         2.01        50.04         5.98        37.05 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05        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-3860 
       10.06        33.07        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       12.99         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       26.01         7.96        13.94        34.03        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X 
       17.03        14.99        21.99        15.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 
       37.02        39.98        41.00        40.96         5.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D 
        0.20        16.44        14.50        16.31        33.01        17.85 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        1.41         5.65         5.13        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 
        3.19         1.61        12.69         3.06        12.20        14.30 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 
       49.08         1.91        25.02         8.02        29.06        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
        5.03        15.02        15.02        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       45.40        56.09        20.19         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 
       17.85        12.49         1.48        12.43         4.80        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
      130.65        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 
        6.12        26.47        31.96         1.55        16.24        13.25 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
        8.35        82.39        85.48        63.62        61.91        36.00 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       91.79        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        30.28        13.55        19.10 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 
       14.50        15.39        10.39        65.98        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 
        7.07        36.03        20.05        24.00        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 
       34.03        50.04        15.95        13.94        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 
       37.02        19.99         1.02        17.95         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        36.03        14.04         3.98        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 
       12.00        10.98         1.94        38.96        41.00        38.56 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        0.72        10.19         6.05         4.73        12.39        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       11.01         5.03        13.97        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
        5.03        41.36        51.48        32.61         2.40        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       17.69        16.31        16.41        28.57         0.39         0.66 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.76        18.28        26.43 

$`DEL PEAK 46(22Q13.32) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       15.62        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 
       42.90        24.33        37.05        37.25        37.02        32.45 
TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       32.91        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        25.18        24.16 
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-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
        1.02        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       34.03        29.00         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        14.93         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       36.03        53.00        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       24.00        20.98        34.03        16.08        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        38.04         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98         1.02        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-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37        15.52 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.79         0.72        27.42        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.95        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
       19.33        18.84       109.28        75.95        58.39        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      106.75        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01        11.74         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07        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         9.99        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-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       13.02        22.03        22.98        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         2.96        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       12.95        13.05        11.08        12.03        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.42        17.75        18.25         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       16.14        15.58         3.68         4.41        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB 
       24.43        38.20        92.75        49.91         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         0.53        47.41        35.31       133.18        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       55.04        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV 
       13.78        35.80        26.17        74.79        79.69        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        17.85        16.80        32.98         8.42 
TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        11.90        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       43.04        34.49        37.74        10.39        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 
       86.63        11.84        36.03         8.02         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
        2.01        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       32.02         1.02        17.03        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        70.03        64.01        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.04         1.45         0.69        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
        6.97         9.37        78.12         7.17        15.02         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        27.95         5.95         5.29       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
      129.27        24.13         0.49        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        15.85        16.34         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-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       31.30        32.19         0.69         0.53         1.12        12.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                          19.33                           20.20 
[1] "0.2 - 140.4 (19.3)" "0.0 - 148.0 (20.2)"
[1] "hr=" "1.4"
D73V2, continuous
D73V3, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   158  66
  DEL PEAK 46(22Q13.32) WILD-TYPE 288  96
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    158   66
  DEL PEAK 46(22Q13.32) WILD-TYPE  288   96
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON                            158                             288
  RECTUM                            66                              96
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 46(22Q13.32) MUTATED        29        0        9        59         1
  DEL PEAK 46(22Q13.32) WILD-TYPE      75        1       27       114         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(22Q13.32) MUTATED           1        10         12         31
  DEL PEAK 46(22Q13.32) WILD-TYPE         2        16          6         52
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(22Q13.32) MUTATED           24       34        11         0
  DEL PEAK 46(22Q13.32) WILD-TYPE         30       29        15         2
D73V4, multiclass
            clus
vv           DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  STAGE I                               29                              75
  STAGE IA                               0                               1
  STAGE II                               9                              27
  STAGE IIA                             59                             114
  STAGE IIB                              1                               9
  STAGE IIC                              1                               2
  STAGE III                             10                              16
  STAGE IIIA                            12                               6
  STAGE IIIB                            31                              52
  STAGE IIIC                            24                              30
  STAGE IV                              34                              29
  STAGE IVA                             11                              15
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 46(22Q13.32) MUTATED     4  37 159  27
  DEL PEAK 46(22Q13.32) WILD-TYPE  16  69 258  40
D73V5, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  T1                             4                              16
  T2                            37                              69
  T3                           159                             258
  T4                            27                              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 46(22Q13.32) MUTATED   104  71  51
  DEL PEAK 46(22Q13.32) WILD-TYPE 241  79  64
D73V6, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  N0                           104                             241
  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"
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   154  44
  DEL PEAK 46(22Q13.32) WILD-TYPE 296  44
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    154   44
  DEL PEAK 46(22Q13.32) WILD-TYPE  296   44
   clus
vv  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  0                           154                             296
  1                            44                              44
[1] 2 2
[1] FALSE
D73V8, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   101 126
  DEL PEAK 46(22Q13.32) WILD-TYPE 186 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    101  126
  DEL PEAK 46(22Q13.32) WILD-TYPE  186  199
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  FEMALE                           101                             186
  MALE                             126                             199
[1] 2 2
[1] FALSE
D73V9, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   170  10
  DEL PEAK 46(22Q13.32) WILD-TYPE 276  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    170   10
  DEL PEAK 46(22Q13.32) WILD-TYPE  276   18
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  NO                            170                             276
  YES                            10                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                    146
  DEL PEAK 46(22Q13.32) WILD-TYPE                  236
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                              11
  DEL PEAK 46(22Q13.32) WILD-TYPE                            49
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                      62
  DEL PEAK 46(22Q13.32) WILD-TYPE                    84
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                4
  DEL PEAK 46(22Q13.32) WILD-TYPE                              9
D73V10, multiclass
                                clus
vv                               DEL PEAK 46(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                     146
  COLON MUCINOUS ADENOCARCINOMA                             11
  RECTAL ADENOCARCINOMA                                     62
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       236
  COLON MUCINOUS ADENOCARCINOMA                               49
  RECTAL ADENOCARCINOMA                                       84
  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 46(22Q13.32) MUTATED   155   2  17  12
  DEL PEAK 46(22Q13.32) WILD-TYPE 287   3  20  17
D73V11, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  R0                           155                             287
  R1                             2                               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"
D73V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(22Q13.32) MUTATED                                  1     4
  DEL PEAK 46(22Q13.32) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(22Q13.32) MUTATED                          26   101
  DEL PEAK 46(22Q13.32) WILD-TYPE                        38   191
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 46(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 46(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     38
  WHITE                                                        191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED     3 122
  DEL PEAK 46(22Q13.32) WILD-TYPE   2 226
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED      3  122
  DEL PEAK 46(22Q13.32) WILD-TYPE    2  226
                        clus
vv                       DEL PEAK 46(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           122
                        clus
vv                       DEL PEAK 46(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             226
[1] 2 2
[1] FALSE
