[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"            "-oTCOADREAD-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/COADREAD-TP/11541489/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/11549100/transformed.cor.cli.txt"

nPatients in clinical file=620, in cluster file=615, common to both=604
[1]  73 604
[1] "AMP PEAK  1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          143                           461 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          143                           461 
[1] "AMP PEAK  2(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          137                           467 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          137                           467 
[1] "AMP PEAK  3(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         488 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         488 
[1] "AMP PEAK  4(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           63                           541 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           63                           541 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          152                           452 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          152                           452 
[1] "AMP PEAK  6(7P21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          357                           247 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          357                           247 
[1] "AMP PEAK  7(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           208                            396 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           208                            396 
[1] "AMP PEAK  8(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           252                            352 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           252                            352 
[1] "AMP PEAK  9(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          325                           279 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          325                           279 
[1] "AMP PEAK 10(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           362                            242 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           362                            242 
[1] "AMP PEAK 11(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            38                            566 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            38                            566 
[1] "AMP PEAK 12(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           135                            469 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           135                            469 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            149                             455 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            149                             455 
[1] "AMP PEAK 14(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            393                             211 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            393                             211 
[1] "AMP PEAK 15(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           388                            216 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           388                            216 
[1] "AMP PEAK 16(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           391                            213 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           391                            213 
[1] "AMP PEAK 17(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            562 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            562 
[1] "AMP PEAK 18(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           169                            435 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           169                            435 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         157                          447 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         157                          447 
[1] "AMP PEAK 20(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           140                            464 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           140                            464 
[1] "AMP PEAK 21(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           109                            495 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           109                            495 
[1] "AMP PEAK 22(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         136                          468 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         136                          468 
[1] "AMP PEAK 23(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           274                            330 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           274                            330 
[1] "AMP PEAK 24(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            355                             249 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            355                             249 
[1] "AMP PEAK 25(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            459                             145 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            459                             145 
[1] "AMP PEAK 26(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         461                          143 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         461                          143 
[1] "AMP PEAK 27(20Q13.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            464                             140 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            464                             140 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           239                            365 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           239                            365 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        172                         432 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        172                         432 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          171                           433 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          171                           433 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         583 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         583 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           569 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           569 
[1] "DEL PEAK  6(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           90                           514 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           90                           514 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          116                           488 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          116                           488 
[1] "DEL PEAK  8(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            62                            542 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            62                            542 
[1] "DEL PEAK  9(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          193                           411 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          193                           411 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          215                           389 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          215                           389 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          224                           380 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          224                           380 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          153                           451 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          153                           451 
[1] "DEL PEAK 13(5Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          182                           422 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          182                           422 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          184                           420 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          184                           420 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           526 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           526 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         513 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         513 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           588 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           588 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          284                           320 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          284                           320 
[1] "DEL PEAK 19(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        296                         308 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        296                         308 
[1] "DEL PEAK 20(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           557 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           557 
[1] "DEL PEAK 21(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           82                           522 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           82                           522 
[1] "DEL PEAK 22(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            492 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            492 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           135                            469 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           135                            469 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            157                             447 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            157                             447 
[1] "DEL PEAK 25(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           154                            450 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           154                            450 
[1] "DEL PEAK 26(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           109                            495 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           109                            495 
[1] "DEL PEAK 27(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            89                            515 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            89                            515 
[1] "DEL PEAK 28(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             88                             516 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             88                             516 
[1] "DEL PEAK 29(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           206                            398 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           206                            398 
[1] "DEL PEAK 30(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           212                            392 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           212                            392 
[1] "DEL PEAK 31(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           246                            358 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           246                            358 
[1] "DEL PEAK 32(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           243                            361 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           243                            361 
[1] "DEL PEAK 33(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           241                            363 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           241                            363 
[1] "DEL PEAK 34(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            231                             373 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            231                             373 
[1] "DEL PEAK 35(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            67                            537 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            67                            537 
[1] "DEL PEAK 36(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            81                            523 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            81                            523 
[1] "DEL PEAK 37(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         361                          243 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         361                          243 
[1] "DEL PEAK 38(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            94                            510 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            94                            510 
[1] "DEL PEAK 39(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            363                             241 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            363                             241 
[1] "DEL PEAK 40(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           408                            196 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           408                            196 
[1] "DEL PEAK 41(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           425                            179 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           425                            179 
[1] "DEL PEAK 42(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           420                            184 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           420                            184 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            95                            509 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            95                            509 
[1] "DEL PEAK 44(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           132                            472 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           132                            472 
[1] "DEL PEAK 45(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           209                            395 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           209                            395 
[1] "DEL PEAK 46(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            222                             382 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            222                             382 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 604 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
         154          160         1126         1419         1331         1321 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
         711          541         1286         1366         1068         1387 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
          NA          472         1127         1133          488         1054 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
        1111           NA          987         1001          962          926 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
         888         1020          718          672          671          995 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         887          824          685          734          255          763 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
         766          735          627          662          751          742 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
         726          612          598          617           NA           NA 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
          NA         1595          293           NA           31           NA 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
          31         1127           31         1065         1765         1946 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
         212           31           NA         1186           31          276 
TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
         731           NA         1127         1096          245          580 
TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
          NA           NA          580         1035          882          882 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
         791          395           30          426         1034          639 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
          NA          730          546          911          700          638 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
         608          424          608         1856         2375          184 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
         212         1643           NA          426           28         1522 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 
        1431         1430          457           NA          182           NA 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 
        1127          578           NA           NA           NA           NA 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        2587          821           NA          579           30           30 
TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        1066           NA           NA          761           31          547 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
         485         1186         1124         1126          454           NA 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
         518           30           NA         1006           NA         1096 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
         975           30          945          945         1612          518 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 
         731           NA          912           NA          549          943 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
          NA          395          730         1004          791          730 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
          NA          638         1035           61          669          489 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        1551          397         1036          791          761          730 
TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
         822           NA          580           NA          822          424 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
        1157          578          913         1035          549          549 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
         518           NA          822         1278           30          518 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
         456          669         1064          457          457           30 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
         974          365          943          943           NA           31 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1065           31         1005         1065          791         1126 
TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
          NA           NA         1581           NA         1216           NA 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
          NA           28           NA         1247         1216           NA 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
        1246            2          650          128         1720           24 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
          22           48           31            3           23            6 
TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
          NA           13           14           28          441          824 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
          NA           NA          479            6          652          542 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
         158          168          209         2289         1532         1776 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
          NA           NA         1002           NA         2549           NA 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        1977           NA         1868           NA           NA           NA 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
          NA           NA           NA           NA           NA           NA 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
          68           93           65           99          100            2 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
           8           10            3           41          534         3116 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1227         2134          475         1466         1561          669 
TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
          NA           NA           NA           89           61         3780 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
         701          609         1126          244          792          244 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
         822          396          884          670          699          915 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
         487          457           NA          457          457          518 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
         457          365          427          883          488          669 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
         456          395          396          457          427          335 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
         394          397          337          337          335          306 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
         366          456          373          596          411          350 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
         614          621          540          555           40          241 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
         460          543          137          521          380          491 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
         474          229          377          308          378          435 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
         275          287          354          408           46          365 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
         346          312         3641          743         1162         3974 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
        2821         1518          405          383         4270          228 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        1348         4000         4126          236         4233          186 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
         427          805         2475         3648         1094         1849 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
        3561         2988         2895           NA          407           NA 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
         415          409           NA         1091           47          496 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
         900          494         1024           39           16         1077 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
         591         3275           NA          254         2506           NA 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        2268         1310         1882         1631         1359         1674 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
        1574         1372         1199         1093         1117         1095 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
         804          672          792          419         1089          796 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
        2792           NA         1434         1606          125           NA 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
         320           85          182          170           40          158 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
         167          821          526          202          449          921 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        2038          734          546          524         1309          412 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
         581          387         1148           NA          441          257 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
         468          609          316         2635         2007          360 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
          NA          365          974          244          215           31 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
          61           NA           31         1400           NA           NA 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 
        1035           NA         1522          366          184           NA 
TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
          NA           30          485          608           NA          608 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
          NA          243           30          912           31         1003 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
          30           30           NA          608           31           NA 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1124          518          396         1065          426           31 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1461           NA          974          608          853         1096 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 
         427           31          518           NA           NA           30 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
         638          424          183          790          700         1126 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
         485         1096          276           31          365          943 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        2130         1947          334           NA         1520           NA 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
          NA         1885         1247         1157           15           44 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
          21           22          140           55          310          184 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
         184           NA          212          285          144          425 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        1826          243          334          335          457          395 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
         365          425          457         1095          216          914 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
         394          397          306          161         3846         1258 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        1741         3932          734         1566          992           15 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
          73          625          607          636          517          556 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
         482          538          497          496          499          262 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         350          328          415          531          364          257 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
          NA         1141          952          452           12           31 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
          20           21           16           34           23           14 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=345,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=32,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "PRIMARY.SITE.OF.DISEASE"               
 [3] "NEOPLASM.DISEASESTAGE"                 
 [4] "PATHOLOGY.T.STAGE"                     
 [5] "PATHOLOGY.N.STAGE"                     
 [6] "PATHOLOGY.M.STAGE"                     
 [7] "GENDER"                                
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "COMPLETENESS.OF.RESECTION"             
[11] "NUMBER.OF.LYMPH.NODES"                 
[12] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 604 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 20 105 412  65 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 105 412  65 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 105 412  65 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 105 412  65 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
341 148 112 
[1] "table(vv)"
vv
 N0  N1  N2 
341 148 112 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
341 148 112 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
341 148 112 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q31.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q31.1) MUTATED   107  30
  AMP PEAK  1(1Q31.1) WILD-TYPE 359  79
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          137                           438 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                           30                            79 
$`AMP PEAK  1(1Q31.1) MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
        5.26        37.02        43.76        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-6649 TCGA-A6-6652 
       15.52        36.53        32.45        29.19        24.16        24.69 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3561 TCGA-AA-3660 
       23.87        52.44         5.03        38.99        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 
       54.02         2.01        47.05        47.01        15.02        19.00 
TCGA-AA-3696 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 
        5.03         0.99        33.07        32.05        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3994 
       27.02        12.99        33.01        21.99        13.05        27.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y 
        0.99        32.02        35.01        26.01         2.96        39.98 
TCGA-AD-6888 TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
        4.21         1.02        14.50         0.20         5.52         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         2.24         3.06 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5349 
        0.26        48.20        37.02         8.02        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        14.04        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         7.53        10.13 
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        13.38        11.11        35.41 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA 
       82.39        74.56        61.87        39.42         4.11         5.98 
TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 
       26.99        30.28        24.13        13.55        14.50        15.39 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 
       10.39        32.02        46.03        34.03         6.05        19.99 
TCGA-AG-3882 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        28.04        23.01        37.02        36.03        31.00 
TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       70.03        51.98         1.94        38.96        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
        0.69         0.72        10.19         9.37         4.73        11.01 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 
       13.97        15.02       129.27        24.13        32.61        20.55 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6810 
        8.61        10.78        13.64        11.97         9.96         0.39 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76        18.28        47.08        26.43 

$`AMP PEAK  1(1Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       13.94        37.05        37.25        16.04        34.65        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       19.99        61.02         6.05         6.97        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       50.04        11.01         5.98        37.05        36.00        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 
       37.02        14.93        17.03        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02        15.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        56.55         0.79         0.72         1.58         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.76         0.20         0.43         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        83.80        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 
      100.01        29.56         5.23         3.19         1.94         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.03        16.01        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        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-D5-5540 
       11.01        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       11.51        20.19        20.42        17.75        18.25         7.92 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 
        4.50        17.13        16.14        15.58        12.39         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26        24.43        38.20       130.65        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-A28E 
        7.76       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       60.79       117.07        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
        0.53        19.43       107.67        28.21         8.35        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       43.07        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       52.80        10.98        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.19         5.49        17.29         6.64        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        43.04        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       10.39         8.45        20.02        86.63        65.98        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         1.02         2.01 
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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-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-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A016 
       20.98        13.94         6.02        25.97        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
        1.02        12.00        64.01        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         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97        13.97        60.03         7.99        10.98        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        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-6883 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.51        17.46         8.45        37.51        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
        1.02         0.66         0.53         1.12         0.46        55.76 

  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       19.590                        17.625 
[1] "0.2 - 129.3 (19.6)" "0.1 - 140.4 (17.6)"
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    94  47
  AMP PEAK  1(1Q31.1) WILD-TYPE 344 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     94   47
  AMP PEAK  1(1Q31.1) WILD-TYPE  344  115
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON                           94                           344
  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        17        0        7        35         2
  AMP PEAK  1(1Q31.1) WILD-TYPE      85        1       29       136         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         14         60
                               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         36       40        19         2
D1V4, multiclass
            clus
vv           AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  STAGE I                             17                            85
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           35                           136
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           7                            14
  STAGE IIIB                          18                            60
  STAGE IIIC                          17                            36
  STAGE IV                            21                            40
  STAGE IVA                            8                            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  1(1Q31.1) MUTATED     4  21  96  21
  AMP PEAK  1(1Q31.1) WILD-TYPE  16  84 316  44
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  T1                           4                            16
  T2                          21                            84
  T3                          96                           316
  T4                          21                            44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(1Q31.1) MUTATED    68  38  34
  AMP PEAK  1(1Q31.1) WILD-TYPE 273 110  78
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  N0                          68                           273
  N1                          38                           110
  N2                          34                            78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  1(1Q31.1) MUTATED    96  25   3   0  15
  AMP PEAK  1(1Q31.1) WILD-TYPE 350  49   7   2  48
D1V7, multiclass
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  M0                           96                           350
  M1                           25                            49
  M1A                           3                             7
  M1B                           0                             2
  MX                           15                            48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    60  83
  AMP PEAK  1(1Q31.1) WILD-TYPE 223 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     60   83
  AMP PEAK  1(1Q31.1) WILD-TYPE  223  238
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  FEMALE                          60                           223
  MALE                            83                           238
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                     85
  AMP PEAK  1(1Q31.1) WILD-TYPE                  293
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                               9
  AMP PEAK  1(1Q31.1) WILD-TYPE                            50
                               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
D1V9, multiclass
                                clus
vv                               AMP PEAK  1(1Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    85
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   43
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     293
  COLON MUCINOUS ADENOCARCINOMA                             50
  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"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED     5 138
  AMP PEAK  1(1Q31.1) WILD-TYPE   4 457
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED      5  138
  AMP PEAK  1(1Q31.1) WILD-TYPE    4  457
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  NO                            5                             4
  YES                         138                           457
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q31.1) MUTATED    99   1  11   6
  AMP PEAK  1(1Q31.1) WILD-TYPE 337   4  25  23
D1V11, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  R0                          99                           337
  R1                           1                             4
  R2                          11                            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"
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                          13    78
  AMP PEAK  1(1Q31.1) WILD-TYPE                        43   214
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     78
                                  clus
vv                                 AMP PEAK  1(1Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(2Q33.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2Q33.1) MUTATED   101  28
  AMP PEAK  2(2Q33.1) WILD-TYPE 365  81
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          129                           446 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                           28                            81 
$`AMP PEAK  2(2Q33.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
        5.06        37.02        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       30.44        32.71        29.16        24.16        24.69        23.87 
TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3562 
       24.92         1.02        34.03        29.00        29.00        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       50.04        15.02        37.05         5.03         0.99        35.05 
TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3979 TCGA-AA-A00W TCGA-AA-A01I 
       33.07        24.03        16.08        24.00        14.99        31.00 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        1.02        26.01         2.96        21.37         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
        1.02         0.10         0.20         0.43        16.31         0.20 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 
        6.87         5.13         3.19         0.07         0.26        40.34 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       21.99         8.02        29.06         5.03        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 
       14.04        29.03        21.99        14.99        14.99        11.51 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A280 
        4.50        17.13         7.53        24.43         7.50         7.76 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 
       14.04        26.47        35.97         8.61         1.55         8.35 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       74.56        45.11        39.42        47.15        52.80         4.11 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
        1.32         5.19        17.29        30.28        24.13        17.95 
TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       17.23        10.39         8.45        15.39        86.63        65.98 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3883 
       36.03        46.03         6.05        19.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       17.03         1.02        48.03        28.04         1.02         0.99 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       12.00        31.00        70.03        38.04         0.49         0.69 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
        4.60        10.19        13.97        60.03         7.99        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 
       12.00        15.02        36.00        13.05       129.27         2.40 
TCGA-EI-6508 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 
       20.91        16.31        13.64         9.96        37.51         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.46        18.28        47.08 

$`AMP PEAK  2(2Q33.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 
       37.05        37.25        16.04        32.45        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 
       24.39        20.12        19.66        20.28        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
       36.03         8.05        19.07        19.07        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00        85.05        26.99        19.04         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       36.95        37.02        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        25.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         0.07        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
       15.75        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         3.29         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       48.20        51.32        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
        7.92        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        10.52         2.79         5.98         5.59         5.49 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       26.99         6.64        14.76        67.00        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-6672 
       19.10        12.72        37.74        14.50        20.02        10.39 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
       29.98         1.02        32.98         0.99         0.99        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 
       61.97        41.00         1.45         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 
        6.05         6.97         9.37         4.73        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        13.97         7.10        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       10.78        17.46        11.97         8.45        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                        16.31                         18.05 
[1] "0.1 - 129.3 (16.3)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    88  49
  AMP PEAK  2(2Q33.1) WILD-TYPE 350 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     88   49
  AMP PEAK  2(2Q33.1) WILD-TYPE  350  113
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON                           88                           350
  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        28         0
  AMP PEAK  2(2Q33.1) WILD-TYPE      81        1       28       143        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2Q33.1) MUTATED           2         6          4         21
  AMP PEAK  2(2Q33.1) WILD-TYPE         1        20         17         57
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(2Q33.1) MUTATED           21       14         6         1
  AMP PEAK  2(2Q33.1) WILD-TYPE         32       47        21         1
D2V4, multiclass
            clus
vv           AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  STAGE I                             21                            81
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           28                           143
  STAGE IIB                            0                            10
  STAGE IIC                            2                             1
  STAGE III                            6                            20
  STAGE IIIA                           4                            17
  STAGE IIIB                          21                            57
  STAGE IIIC                          21                            32
  STAGE IV                            14                            47
  STAGE IVA                            6                            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
  AMP PEAK  2(2Q33.1) MUTATED     3  23  96  14
  AMP PEAK  2(2Q33.1) WILD-TYPE  17  82 316  51
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  T1                           3                            17
  T2                          23                            82
  T3                          96                           316
  T4                          14                            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  2(2Q33.1) MUTATED    62  34  39
  AMP PEAK  2(2Q33.1) WILD-TYPE 279 114  73
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  N0                          62                           279
  N1                          34                           114
  N2                          39                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  2(2Q33.1) MUTATED    92  18   3   1  20
  AMP PEAK  2(2Q33.1) WILD-TYPE 354  56   7   1  43
D2V7, multiclass
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  M0                           92                           354
  M1                           18                            56
  M1A                           3                             7
  M1B                           1                             1
  MX                           20                            43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    65  72
  AMP PEAK  2(2Q33.1) WILD-TYPE 218 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     65   72
  AMP PEAK  2(2Q33.1) WILD-TYPE  218  249
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  FEMALE                          65                           218
  MALE                            72                           249
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                     79
  AMP PEAK  2(2Q33.1) WILD-TYPE                  299
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                               9
  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
D2V9, multiclass
                                clus
vv                               AMP PEAK  2(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                    79
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     299
  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"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED     4 133
  AMP PEAK  2(2Q33.1) WILD-TYPE   5 462
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED      4  133
  AMP PEAK  2(2Q33.1) WILD-TYPE    5  462
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  NO                            4                             5
  YES                         133                           462
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2Q33.1) MUTATED    93   2   8   9
  AMP PEAK  2(2Q33.1) WILD-TYPE 343   3  28  20
D2V11, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  R0                          93                           343
  R1                           2                             3
  R2                           8                            28
  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                          18    73
  AMP PEAK  2(2Q33.1) WILD-TYPE                        38   219
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                     73
                                  clus
vv                                 AMP PEAK  2(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      219
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(5P12) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(5P12) MUTATED    86  26
  AMP PEAK  3(5P12) WILD-TYPE 380  83
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        112                         463 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                         26                          83 
$`AMP PEAK  3(5P12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 
        5.06        43.76        43.43        44.91        45.60        37.25 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 
       32.45        30.44        20.61         5.03        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 
       13.02        24.00         2.01        47.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3856 
       19.00         0.99        37.02        14.93        36.03         0.99 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F 
       17.03        24.03        21.99        50.99        26.01        34.03 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W 
       21.99         0.99        51.98         2.96         2.01        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK 
       40.96         1.58         0.43         0.92         0.20         6.87 
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         1.94         2.24 
TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       48.20         8.02        16.01        15.02        14.04        29.03 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 
       14.99        13.02        11.01        19.59        17.75        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 
       14.30        13.41        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        13.38        35.41        46.75        47.15         1.32 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
        6.64        30.28        24.13        37.74        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3731 
       86.63        65.98         1.02        46.03        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00H 
       17.03        28.04        36.03         1.02        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       36.03        12.00        31.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6158 
       38.04         0.69         0.72        12.99        15.02         7.10 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 
       10.06        57.24         2.40        16.31        11.51         9.96 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       14.86         1.02         0.53         0.76 

$`AMP PEAK  3(5P12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.26        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 
       35.11        13.94        15.52        37.05        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       47.05        15.02        11.01        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         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        36.95        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.99        33.07        32.05        31.07        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-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-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-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-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-A02F TCGA-AA-A02J 
       35.01        26.01        37.02        39.06        39.98         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-6901 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46        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        15.75        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        65.00        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
      100.01         5.23        11.74         3.19         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         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.26        13.51        11.51        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
        1.32         7.92        15.12        17.85         4.50        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.19         5.49        26.99        17.29        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 
       10.39        14.50         8.45        15.39        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         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        14.04         0.99        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        15.95         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 
       64.01        10.98        51.98        49.97        61.97         0.49 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
       10.98        11.01        15.02        12.00        13.97        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45        37.51        31.30         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                       0.20                        0.07 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      95.18                      140.38 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      16.67                       18.05 
[1] "0.2 - 95.2 (16.7)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    76  40
  AMP PEAK  3(5P12) WILD-TYPE 362 122
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     76   40
  AMP PEAK  3(5P12) WILD-TYPE  362  122
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  COLON                         76                         362
  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      84        1       30       144         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         16         66
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(5P12) MUTATED           16       17         6         1
  AMP PEAK  3(5P12) WILD-TYPE         37       44        21         1
D3V4, multiclass
            clus
vv           AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  STAGE I                           18                          84
  STAGE IA                           0                           1
  STAGE II                           6                          30
  STAGE IIA                         27                         144
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          3                          23
  STAGE IIIA                         5                          16
  STAGE IIIB                        12                          66
  STAGE IIIC                        16                          37
  STAGE IV                          17                          44
  STAGE IVA                          6                          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
  AMP PEAK  3(5P12) MUTATED     2  25  76  13
  AMP PEAK  3(5P12) WILD-TYPE  18  80 336  52
D3V5, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  T1                         2                          18
  T2                        25                          80
  T3                        76                         336
  T4                        13                          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  3(5P12) MUTATED    54  32  29
  AMP PEAK  3(5P12) WILD-TYPE 287 116  83
D3V6, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  N0                        54                         287
  N1                        32                         116
  N2                        29                          83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  AMP PEAK  3(5P12) MUTATED    78  19   3   1  12
  AMP PEAK  3(5P12) WILD-TYPE 368  55   7   1  51
D3V7, multiclass
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  M0                         78                         368
  M1                         19                          55
  M1A                         3                           7
  M1B                         1                           1
  MX                         12                          51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    52  64
  AMP PEAK  3(5P12) WILD-TYPE 231 257
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     52   64
  AMP PEAK  3(5P12) WILD-TYPE  231  257
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  FEMALE                        52                         231
  MALE                          64                         257
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                     67
  AMP PEAK  3(5P12) WILD-TYPE                  311
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                               9
  AMP PEAK  3(5P12) WILD-TYPE                            50
                             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
D3V9, multiclass
                                clus
vv                               AMP PEAK  3(5P12) MUTATED
  COLON ADENOCARCINOMA                                  67
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 40
  RECTAL MUCINOUS ADENOCARCINOMA                         0
                                clus
vv                               AMP PEAK  3(5P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   311
  COLON MUCINOUS ADENOCARCINOMA                           50
  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"
D3V10, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED     3 113
  AMP PEAK  3(5P12) WILD-TYPE   6 482
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED      3  113
  AMP PEAK  3(5P12) WILD-TYPE    6  482
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  NO                          3                           6
  YES                       113                         482
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  3(5P12) MUTATED    84   1  13   3
  AMP PEAK  3(5P12) WILD-TYPE 352   4  23  26
D3V11, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  R0                        84                         352
  R1                         1                           4
  R2                        13                          23
  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                          13    53
  AMP PEAK  3(5P12) WILD-TYPE                        43   239
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(5P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                   53
                                  clus
vv                                 AMP PEAK  3(5P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(5Q22.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(5Q22.3) MUTATED    54   7
  AMP PEAK  4(5Q22.3) WILD-TYPE 412 102
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           61                           514 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                            7                           102 
$`AMP PEAK  4(5Q22.3) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
        5.06        44.91        45.60        37.25        34.65        32.45 
TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3715 
       25.08        20.61         5.03        15.02         5.98         0.99 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       14.93        24.03        12.99        13.05        34.06        26.01 
TCGA-AA-3994 TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-4684 
       27.02        40.96         1.58         0.43        15.75        65.00 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 
       49.41        11.74        16.01         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6932 TCGA-DM-A1D0 
       14.99        11.01        17.75         1.32        11.38       130.65 
TCGA-DM-A1D8 TCGA-DM-A28M TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6627 TCGA-NH-A6GB 
       12.59        95.18        13.38        44.68        47.15         5.59 
TCGA-AF-6655 TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A014 
       20.02        19.99         1.02         1.02        25.97        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       12.00        31.00        38.04         0.49         0.69         0.72 
TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6465 
       10.06        20.55        16.31        11.51        11.97        37.51 
TCGA-F5-6811 
        1.02 

$`AMP PEAK  4(5Q22.3) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.26        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3977 TCGA-AA-3979 
        2.01        21.99        16.08        50.99        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.98         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        67.00        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        12.72        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
        8.45        15.39        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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        41.00         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46         8.45         9.96        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                       130.65                        140.38 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                        15.02                         18.05 
[1] "0.4 - 130.7 (15.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    43  20
  AMP PEAK  4(5Q22.3) WILD-TYPE 395 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     43   20
  AMP PEAK  4(5Q22.3) WILD-TYPE  395  142
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON                           43                           395
  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         8        0        2        16         1
  AMP PEAK  4(5Q22.3) WILD-TYPE      94        1       34       155         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         19         70
                               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         46       52        22         2
D4V4, multiclass
            clus
vv           AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  STAGE I                              8                            94
  STAGE IA                             0                             1
  STAGE II                             2                            34
  STAGE IIA                           16                           155
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            1                            25
  STAGE IIIA                           2                            19
  STAGE IIIB                           8                            70
  STAGE IIIC                           7                            46
  STAGE IV                             9                            52
  STAGE IVA                            5                            22
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(5Q22.3) MUTATED     1  11  44   7
  AMP PEAK  4(5Q22.3) WILD-TYPE  19  94 368  58
D4V5, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  T1                           1                            19
  T2                          11                            94
  T3                          44                           368
  T4                           7                            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  4(5Q22.3) MUTATED    30  17  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 311 131  97
D4V6, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  N0                          30                           311
  N1                          17                           131
  N2                          15                            97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  4(5Q22.3) MUTATED    41  12   3   0   5
  AMP PEAK  4(5Q22.3) WILD-TYPE 405  62   7   2  58
D4V7, multiclass
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  M0                           41                           405
  M1                           12                            62
  M1A                           3                             7
  M1B                           0                             2
  MX                            5                            58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    30  33
  AMP PEAK  4(5Q22.3) WILD-TYPE 253 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     30   33
  AMP PEAK  4(5Q22.3) WILD-TYPE  253  288
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  FEMALE                          30                           253
  MALE                            33                           288
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                     40
  AMP PEAK  4(5Q22.3) WILD-TYPE                  338
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                               3
  AMP PEAK  4(5Q22.3) WILD-TYPE                            56
                               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
D4V9, multiclass
                                clus
vv                               AMP PEAK  4(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                    40
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   20
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     338
  COLON MUCINOUS ADENOCARCINOMA                             56
  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"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED     1  62
  AMP PEAK  4(5Q22.3) WILD-TYPE   8 533
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED      1   62
  AMP PEAK  4(5Q22.3) WILD-TYPE    8  533
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  NO                            1                             8
  YES                          62                           533
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(5Q22.3) MUTATED    44   0   7   0
  AMP PEAK  4(5Q22.3) WILD-TYPE 392   5  29  29
D4V11, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  R0                          44                           392
  R1                           0                             5
  R2                           7                            29
  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                           7    34
  AMP PEAK  4(5Q22.3) WILD-TYPE                        49   258
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  4(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(6P21.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(6P21.1) MUTATED   113  27
  AMP PEAK  5(6P21.1) WILD-TYPE 353  82
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          140                           435 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           27                            82 
$`AMP PEAK  5(6P21.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       43.43        44.91        36.53        32.45        30.44        29.19 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A56B 
       22.52        25.08        25.18        20.61        23.87        52.44 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3561 
       29.00        29.00        12.99        13.02        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       19.99         2.01        15.02        37.05        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 
       35.05        17.03         0.99        24.03        27.02         2.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F 
       20.98        21.99        27.02         7.96        13.94        34.03 
TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 
       27.02        31.00         2.96        40.96         1.02         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 
       14.50         0.95         0.20         5.19         5.65        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00         1.35        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       29.06        22.98        30.08        16.01         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 
       13.02        15.02        19.59        13.51        11.51         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       15.12        17.13        12.49         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H 
       13.41        11.38        13.32         7.50        14.04       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       98.24        95.18         8.61        13.38        13.45         1.55 
TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6311 
        0.53        28.21         8.35        82.39        45.11        39.42 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 
       91.79        46.75        10.98         1.32        30.28        24.13 
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-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 
       65.98         1.02        24.00        46.03         6.05        19.99 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 
       19.99        29.98         1.02         1.02        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 
        0.99        36.03         9.07        12.00        31.00         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 
       10.19         6.05         9.37        10.98        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       15.02        36.00        13.05       129.27        24.13        51.48 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       20.55        15.85        17.69        37.51        14.86         0.39 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        16.04        34.65        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       29.16        27.09        24.13         8.38        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       34.03        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       17.95        29.95        23.01        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       50.04        47.05        47.01        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 
       36.00         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        53.00        17.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 
       34.06        26.01        25.02        24.00        19.07        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-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        15.02        15.02         0.99        32.02        12.00 
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-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.72         1.58         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        15.75        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        70.16        48.20        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 
        8.02        26.04        27.02        22.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        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-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       14.99        12.26        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        7.92        17.85         4.50        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59       140.38        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-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       35.97        60.79        11.11        13.64         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       16.31        29.59        16.24        33.67         1.28        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       19.43       107.67        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        47.15        52.80         4.11        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
        6.64        14.76        67.00        17.95        17.23        13.55 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       12.72         8.45        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-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       15.95         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-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-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       37.02        15.95         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-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04         0.49         1.45         0.69         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         4.73        13.97        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        13.97         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
       10.06         5.29       126.44        41.36        57.24        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-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       15.735                        18.050 
[1] "0.2 - 129.3 (15.7)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    98  51
  AMP PEAK  5(6P21.1) WILD-TYPE 340 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     98   51
  AMP PEAK  5(6P21.1) WILD-TYPE  340  111
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  COLON                           98                           340
  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        20        0        4        33         1
  AMP PEAK  5(6P21.1) WILD-TYPE      82        1       32       138         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(6P21.1) MUTATED           1         7          7         25
  AMP PEAK  5(6P21.1) WILD-TYPE         2        19         14         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(6P21.1) MUTATED           19       19        12         1
  AMP PEAK  5(6P21.1) WILD-TYPE         34       42        15         1
D5V4, multiclass
            clus
vv           AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  STAGE I                             20                            82
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           33                           138
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            7                            19
  STAGE IIIA                           7                            14
  STAGE IIIB                          25                            53
  STAGE IIIC                          19                            34
  STAGE IV                            19                            42
  STAGE IVA                           12                            15
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(6P21.1) MUTATED     6  19 112  15
  AMP PEAK  5(6P21.1) WILD-TYPE  14  86 300  50
D5V5, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  T1                           6                            14
  T2                          19                            86
  T3                         112                           300
  T4                          15                            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  5(6P21.1) MUTATED    66  41  44
  AMP PEAK  5(6P21.1) WILD-TYPE 275 107  68
D5V6, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  N0                          66                           275
  N1                          41                           107
  N2                          44                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  5(6P21.1) MUTATED   102  25   5   1  15
  AMP PEAK  5(6P21.1) WILD-TYPE 344  49   5   1  48
D5V7, multiclass
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  M0                          102                           344
  M1                           25                            49
  M1A                           5                             5
  M1B                           1                             1
  MX                           15                            48
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    63  89
  AMP PEAK  5(6P21.1) WILD-TYPE 220 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     63   89
  AMP PEAK  5(6P21.1) WILD-TYPE  220  232
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                          63                           220
  MALE                            89                           232
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                     90
  AMP PEAK  5(6P21.1) WILD-TYPE                  288
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                               8
  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
D5V9, multiclass
                                clus
vv                               AMP PEAK  5(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                            8
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  5(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     288
  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"
D5V10, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED     7 145
  AMP PEAK  5(6P21.1) WILD-TYPE   2 450
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      7  145
  AMP PEAK  5(6P21.1) WILD-TYPE    2  450
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  NO                            7                             2
  YES                         145                           450
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(6P21.1) MUTATED   106   0  14   5
  AMP PEAK  5(6P21.1) WILD-TYPE 330   5  22  24
D5V11, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  R0                         106                           330
  R1                           0                             5
  R2                          14                            22
  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                          13    82
  AMP PEAK  5(6P21.1) WILD-TYPE                        43   210
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     82
                                  clus
vv                                 AMP PEAK  5(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(7P21.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P21.3) MUTATED   273  66
  AMP PEAK  6(7P21.3) WILD-TYPE 193  43
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          339                           236 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                           66                            43 
$`AMP PEAK  6(7P21.3) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        5.06         5.26        37.02        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       29.16        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       20.61        24.69        23.87        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01        58.03         6.97        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       36.03        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       13.02        24.00        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 
        6.05        54.02         2.01        14.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        0.99        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
        0.99        32.05         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 
       27.02        29.98        18.05        31.00        24.00        24.00 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 
       20.98        21.99        16.08        34.06        26.01        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       27.02        13.94        19.00        34.03        17.03        42.02 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       17.03        15.02        32.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       51.98         2.96         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
        0.95        15.75         0.20        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25        50.37        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       61.41        49.41        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 
        1.94         3.06         2.14         3.25         3.29         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56       102.44        40.34        21.99        20.02         8.02 
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-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        29.03        16.04        14.99        12.99        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 
       11.01        11.08        11.08        11.01        10.06        19.59 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       11.51        17.75         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
        4.50        17.13        12.49         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        10.26        24.43        38.20 
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-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
      131.51         7.76         6.12        14.04        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 
       95.18         8.61        13.38        13.45         1.55        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
        0.53        35.41       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       74.56        61.87        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 
       35.93        36.72        36.00        26.43        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        47.15         4.11         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        5.19         6.64        30.28        67.00        24.13        17.95 
TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       17.23        12.72        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 
       15.39        20.02        86.63        65.98         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       24.00        46.03        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99        19.99        29.98         0.99         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       17.03        35.01         1.02        48.03        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 
        1.02        17.03         0.99         6.02        25.97        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-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       10.98         1.94        38.96        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
        0.72         4.60        10.19         6.05         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        60.03         7.99        10.98        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.00        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
       24.13         0.49         2.40        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.31        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        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`AMP PEAK  6(7P21.3) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        17.79        42.28        15.52        37.05 
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       14.53        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        21.76        24.39        20.12        19.66 
TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       61.84         3.02        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       29.00         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       20.98        13.94         6.97         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3821 
       47.01        26.99        19.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       17.98        15.95        38.99        17.03        33.07        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00         2.01        12.99        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
        2.01        34.03         2.01        50.99        13.05        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       24.00        19.07         7.96        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       18.05         4.01        27.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A024 
       38.07         1.02        35.01         1.02        35.01        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       39.98        22.03        41.00        18.05         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D 
        0.72         0.76         0.92        27.09        21.44         5.52 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 
       58.39         1.41         5.65        32.94         5.13         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
      100.01        11.74         2.24         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
        0.10        70.16        15.62        48.20        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 
       30.08        15.02        12.00        21.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        13.05        12.03        14.99        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       20.19        20.42        18.25        16.14        15.58        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        11.38       119.70 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      130.65        13.32       135.65       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
      119.93        60.79        98.24        11.11        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 
       35.87        16.31        29.59        16.24         1.28        19.43 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 
        8.35        43.07        53.62        51.75        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        52.80        10.98        10.52         2.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 
        5.49        26.99        17.29        14.76        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         2.01         1.02        34.03         2.01        50.04 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         1.02        32.98         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A002 
       13.02        14.01        32.02        28.04        14.04        20.98 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
       13.94        23.01        37.02        64.01        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-4957 
       61.97        41.00         1.45         1.81         6.97        13.97 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       15.02        30.05        12.95        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 
       19.96        17.00        16.41         8.61        17.46        37.51 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.12 

  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                        17.03                         19.07 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   247 108
  AMP PEAK  6(7P21.3) WILD-TYPE 191  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    247  108
  AMP PEAK  6(7P21.3) WILD-TYPE  191   54
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  COLON                          247                           191
  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        56        1       19        77         3
  AMP PEAK  6(7P21.3) WILD-TYPE      46        0       17        94         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(7P21.3) MUTATED           2        15         15         58
  AMP PEAK  6(7P21.3) WILD-TYPE         1        11          6         20
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(7P21.3) MUTATED           38       42        21         1
  AMP PEAK  6(7P21.3) WILD-TYPE         15       19         6         1
D6V4, multiclass
            clus
vv           AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  STAGE I                             56                            46
  STAGE IA                             1                             0
  STAGE II                            19                            17
  STAGE IIA                           77                            94
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           15                            11
  STAGE IIIA                          15                             6
  STAGE IIIB                          58                            20
  STAGE IIIC                          38                            15
  STAGE IV                            42                            19
  STAGE IVA                           21                             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  60 244  38
  AMP PEAK  6(7P21.3) WILD-TYPE   7  45 168  27
D6V5, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  T1                          13                             7
  T2                          60                            45
  T3                         244                           168
  T4                          38                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  6(7P21.3) MUTATED   170 107  77
  AMP PEAK  6(7P21.3) WILD-TYPE 171  41  35
D6V6, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  N0                         170                           171
  N1                         107                            41
  N2                          77                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  6(7P21.3) MUTATED   249  52   8   1  41
  AMP PEAK  6(7P21.3) WILD-TYPE 197  22   2   1  22
D6V7, multiclass
     clus
vv    AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  M0                          249                           197
  M1                           52                            22
  M1A                           8                             2
  M1B                           1                             1
  MX                           41                            22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   167 190
  AMP PEAK  6(7P21.3) WILD-TYPE 116 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    167  190
  AMP PEAK  6(7P21.3) WILD-TYPE  116  131
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  FEMALE                         167                           116
  MALE                           190                           131
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                    222
  AMP PEAK  6(7P21.3) WILD-TYPE                  156
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                              25
  AMP PEAK  6(7P21.3) WILD-TYPE                            34
                               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
D6V9, multiclass
                                clus
vv                               AMP PEAK  6(7P21.3) MUTATED
  COLON ADENOCARCINOMA                                   222
  COLON MUCINOUS ADENOCARCINOMA                           25
  RECTAL ADENOCARCINOMA                                  102
  RECTAL MUCINOUS ADENOCARCINOMA                           5
                                clus
vv                               AMP PEAK  6(7P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     156
  COLON MUCINOUS ADENOCARCINOMA                             34
  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"
D6V10, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED     8 349
  AMP PEAK  6(7P21.3) WILD-TYPE   1 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED      8  349
  AMP PEAK  6(7P21.3) WILD-TYPE    1  246
     clus
vv    AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  NO                            8                             1
  YES                         349                           246
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(7P21.3) MUTATED   256   4  25  14
  AMP PEAK  6(7P21.3) WILD-TYPE 180   1  11  15
D6V11, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  R0                         256                           180
  R1                           4                             1
  R2                          25                            11
  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                          38   183
  AMP PEAK  6(7P21.3) WILD-TYPE                        18   109
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(7P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 38
  WHITE                                                    183
                                  clus
vv                                 AMP PEAK  6(7P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   18
  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"

Clustering(7) Variable = AMP PEAK  7(8P11.23) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.23) MUTATED   155  40
  AMP PEAK  7(8P11.23) WILD-TYPE 311  69
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           195                            380 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                            40                             69 
$`AMP PEAK  7(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 
        5.06         5.26        43.43        17.79        45.60        13.94 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       34.65        32.45        32.91        32.71        29.16        27.09 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3496 
       25.18        24.16        20.28         9.63        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3534 
       35.01         6.97         1.02        36.03        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       26.01        12.99        33.99        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
        5.98        37.05        19.00         5.03        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 
        0.99        36.95        17.03        31.07        31.07        24.03 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00K 
       18.05        12.99        24.00        34.06        24.00        18.05 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
        0.99        21.99         0.99         1.02        37.02        51.98 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 
        0.92         0.07         1.58         0.10         0.43        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       16.31        21.44         5.19         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 
       83.80        22.36        62.79        61.41        49.41         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      102.44        15.62        48.20        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02         8.02         8.02        22.98        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        15.02        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        13.02        11.01        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       10.06        11.51        20.19         1.32         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 
       16.14         7.53        12.43        14.30         9.04        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 
       10.26       119.70        38.20         7.50        44.32         6.12 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 
      117.07        98.24        13.45         6.18        16.24        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 
       61.87        53.62        45.11        39.42        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       47.15         4.11         5.59        17.29         6.64        30.28 
TCGA-WS-AB45 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       67.00        37.74        20.02        10.39        65.98        36.03 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 
        1.02        24.00         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         0.99 
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         0.49         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        60.03         7.99 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
       15.02        36.00         7.10        13.05        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        37.51        14.86         1.02         0.69 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.46        18.28        47.08 

$`AMP PEAK  7(8P11.23) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       35.11        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       19.66        16.24        24.92        61.84        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        1.02         3.02         1.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       13.94        61.02         2.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        36.00        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       39.06         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         1.02         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        14.50         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
        1.41        65.00         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        5.23        11.74         3.25         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
        1.35        17.56        40.34        70.16        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
        2.93       124.27        23.05        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       29.06        22.03        30.08        17.03        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       16.04        15.02        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 
       12.03        14.99        12.26        19.59        13.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       17.75        18.25         7.92        15.12        17.85        12.49 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58        12.39        10.13         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
        1.51        12.00        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79        95.18         8.61        13.38        11.11        13.64 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       82.39        23.51        74.56        44.68        55.04        51.75 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        36.00        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       35.80        26.17        91.79        52.80        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         1.32         5.19         5.49        26.99 
TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       14.76        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        10.39        14.50         8.45        15.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       86.63        11.84        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        2.01         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 
        1.02        17.03        13.02        14.01        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-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         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.05         6.97        13.97        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       12.99        12.00        13.97        30.05        12.95        10.06 
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 
                          0.07                           0.10 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                        119.70                         140.38 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                        17.000                         18.015 
[1] "0.1 - 119.7 (17.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   155  53
  AMP PEAK  7(8P11.23) WILD-TYPE 283 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    155   53
  AMP PEAK  7(8P11.23) WILD-TYPE  283  109
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  COLON                           155                            283
  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        52         4
  AMP PEAK  7(8P11.23) WILD-TYPE      65        1       19       119         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.23) MUTATED           3         8          6         23
  AMP PEAK  7(8P11.23) WILD-TYPE         0        18         15         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.23) MUTATED           23       22         9         0
  AMP PEAK  7(8P11.23) WILD-TYPE         30       39        18         2
D7V4, multiclass
            clus
vv           AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  STAGE I                              37                             65
  STAGE IA                              0                              1
  STAGE II                             17                             19
  STAGE IIA                            52                            119
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                             8                             18
  STAGE IIIA                            6                             15
  STAGE IIIB                           23                             55
  STAGE IIIC                           23                             30
  STAGE IV                             22                             39
  STAGE IVA                             9                             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  7(8P11.23) MUTATED     4  38 141  24
  AMP PEAK  7(8P11.23) WILD-TYPE  16  67 271  41
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  T1                            4                             16
  T2                           38                             67
  T3                          141                            271
  T4                           24                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(8P11.23) MUTATED   118  46  42
  AMP PEAK  7(8P11.23) WILD-TYPE 223 102  70
D7V6, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  N0                          118                            223
  N1                           46                            102
  N2                           42                             70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  7(8P11.23) MUTATED   147  26   5   0  28
  AMP PEAK  7(8P11.23) WILD-TYPE 299  48   5   2  35
D7V7, multiclass
     clus
vv    AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  M0                           147                            299
  M1                            26                             48
  M1A                            5                              5
  M1B                            0                              2
  MX                            28                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED    94 114
  AMP PEAK  7(8P11.23) WILD-TYPE 189 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED     94  114
  AMP PEAK  7(8P11.23) WILD-TYPE  189  207
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  FEMALE                           94                            189
  MALE                            114                            207
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                    139
  AMP PEAK  7(8P11.23) WILD-TYPE                  239
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                              16
  AMP PEAK  7(8P11.23) WILD-TYPE                            43
                                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
D7V9, multiclass
                                clus
vv                               AMP PEAK  7(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                    139
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  7(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      239
  COLON MUCINOUS ADENOCARCINOMA                              43
  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"
D7V10, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED     4 204
  AMP PEAK  7(8P11.23) WILD-TYPE   5 391
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED      4  204
  AMP PEAK  7(8P11.23) WILD-TYPE    5  391
     clus
vv    AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  NO                             4                              5
  YES                          204                            391
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.23) MUTATED   142   1  16  15
  AMP PEAK  7(8P11.23) WILD-TYPE 294   4  20  14
D7V11, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  R0                          142                            294
  R1                            1                              4
  R2                           16                             20
  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                          18   112
  AMP PEAK  7(8P11.23) WILD-TYPE                        38   180
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     112
                                  clus
vv                                 AMP PEAK  7(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(8P11.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(8P11.21) MUTATED   191  47
  AMP PEAK  8(8P11.21) WILD-TYPE 275  62
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           238                            337 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                            47                             62 
$`AMP PEAK  8(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5657 
       35.11        45.60        13.94        34.65        32.45        31.63 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 
       23.61        32.71        29.16        27.09        25.18        24.16 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       20.28        61.84         9.63         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 
       35.01         6.97         1.02        36.03        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01        12.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        19.99        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 
        0.99        36.95        17.03        31.07        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 
       18.05         2.01        12.99        24.00        16.08        34.06 
TCGA-AA-3979 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z 
       24.00        19.00        18.05         0.99        17.03        21.99 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
        1.02        37.02        51.98         0.92        41.00         0.07 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
        1.58         0.10         0.43         0.92        27.09        21.44 
TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
        5.19        32.94         5.13        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       61.41        49.41         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 
        2.24         3.06         2.14         0.07         1.35       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       15.62        48.20        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        8.02         8.02        27.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 
       15.02         5.03        15.02        15.02        15.02        29.03 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        13.02        11.01        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       10.06        11.51        20.19         1.32         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04        13.41        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K 
      130.65         7.50        44.32         6.12       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
        8.61        13.64        13.45         6.18        16.31        16.24 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 
        8.35        74.56        43.07        53.62        44.68        45.11 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       39.42        26.43        46.75        47.15         4.11        10.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-6655 
        5.59        17.29         6.64        30.28        67.00        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       10.39        65.98        36.03         1.02        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        2.01         0.99        32.98         1.02        36.95         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       48.03        32.02        28.04        14.04         1.02         0.99 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       23.01        15.95         9.07         1.02        31.00        64.01 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98         1.94        38.96        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         9.37         4.73        60.03 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        7.99        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        0.49        17.00        15.85        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       13.64        37.51        14.86         1.02         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK  8(8P11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        42.28        44.91        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       37.25        16.04        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 
       29.19        33.53        22.09        22.06        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        5.03         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3672 
       23.01        13.94        61.02         6.05         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       47.05        11.01        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 
       31.07        53.00        17.03        29.98        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       21.99        50.99        13.05        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        35.01        26.01        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         0.72         1.02 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.76         0.20         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       15.75         0.20        17.82         5.52         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 
       50.37        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         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 
        0.33         0.10        17.56        40.34        70.16        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 
       21.14         2.93       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        14.04        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        14.99        12.26        19.59        13.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       17.75        18.25         7.92        15.12        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
       12.39         9.44        11.64         1.51        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-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        13.38        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        29.59        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       61.87        55.04        51.75        35.93        36.72        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 
       52.80        10.52         2.79         5.98         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.49        26.99        14.76        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       14.50         8.45        15.39        86.63        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 
       32.02         8.02         7.07         2.01        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         6.05        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 
       19.99        17.03        13.02        35.01        14.01        19.99 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       37.02        36.03        12.00        70.03        10.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00         4.60         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        6.97        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG TCGA-DY-A1H8 
       12.00        30.05        12.95         5.29        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        2.40        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.34        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        31.30         0.39         0.66         0.69         0.53 
TCGA-F5-6861 
        1.12 

  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                         16.31                          18.25 
[1] "0.1 - 130.7 (16.3)" "0.1 - 140.4 (18.2)"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   182  70
  AMP PEAK  8(8P11.21) WILD-TYPE 256  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    182   70
  AMP PEAK  8(8P11.21) WILD-TYPE  256   92
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  COLON                           182                            256
  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        65         4
  AMP PEAK  8(8P11.21) WILD-TYPE      61        1       15       106         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8P11.21) MUTATED           3        10          9         29
  AMP PEAK  8(8P11.21) WILD-TYPE         0        16         12         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8P11.21) MUTATED           22       34         9         0
  AMP PEAK  8(8P11.21) WILD-TYPE         31       27        18         2
D8V4, multiclass
            clus
vv           AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  STAGE I                              41                             61
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                            65                            106
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            10                             16
  STAGE IIIA                            9                             12
  STAGE IIIB                           29                             49
  STAGE IIIC                           22                             31
  STAGE IV                             34                             27
  STAGE IVA                             9                             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  8(8P11.21) MUTATED     5  45 174  27
  AMP PEAK  8(8P11.21) WILD-TYPE  15  60 238  38
D8V5, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  T1                            5                             15
  T2                           45                             60
  T3                          174                            238
  T4                           27                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  8(8P11.21) MUTATED   142  56  52
  AMP PEAK  8(8P11.21) WILD-TYPE 199  92  60
D8V6, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  N0                          142                            199
  N1                           56                             92
  N2                           52                             60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  8(8P11.21) MUTATED   177  37   6   0  30
  AMP PEAK  8(8P11.21) WILD-TYPE 269  37   4   2  33
D8V7, multiclass
     clus
vv    AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  M0                           177                            269
  M1                            37                             37
  M1A                            6                              4
  M1B                            0                              2
  MX                            30                             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   110 142
  AMP PEAK  8(8P11.21) WILD-TYPE 173 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    110  142
  AMP PEAK  8(8P11.21) WILD-TYPE  173  179
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  FEMALE                          110                            173
  MALE                            142                            179
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                    163
  AMP PEAK  8(8P11.21) WILD-TYPE                  215
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                              19
  AMP PEAK  8(8P11.21) WILD-TYPE                            40
                                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
D8V9, multiclass
                                clus
vv                               AMP PEAK  8(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                    163
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  8(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      215
  COLON MUCINOUS ADENOCARCINOMA                              40
  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"
D8V10, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED     3 249
  AMP PEAK  8(8P11.21) WILD-TYPE   6 346
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED      3  249
  AMP PEAK  8(8P11.21) WILD-TYPE    6  346
     clus
vv    AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  NO                             3                              6
  YES                          249                            346
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(8P11.21) MUTATED   171   2  22  16
  AMP PEAK  8(8P11.21) WILD-TYPE 265   3  14  13
D8V11, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  R0                          171                            265
  R1                            2                              3
  R2                           22                             14
  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                          21   132
  AMP PEAK  8(8P11.21) WILD-TYPE                        35   160
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK  8(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(8Q12.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(8Q12.1) MUTATED   248  59
  AMP PEAK  9(8Q12.1) WILD-TYPE 218  50
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          307                           268 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                           59                            50 
$`AMP PEAK  9(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06         5.26        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       45.60        13.94        15.52        37.25        16.04        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       32.45        32.91        31.63        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       27.09        24.13        25.08        25.18        24.16        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       23.87        20.28         9.63         5.03         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-3562 TCGA-AA-3660 TCGA-AA-3662 
       13.02        24.00        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-3713 TCGA-AA-3715 
        5.98        37.05        36.00         5.03        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 
        0.99        36.95        37.02        17.03        33.07         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-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
        2.01        12.99        24.00        34.03         2.01        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        26.01        24.00        27.02        13.94        19.00 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01G 
       18.05        17.03         0.99        17.03        21.99        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O 
       31.00         1.02        51.98         2.96         5.03         0.92 
TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       41.00         0.07         4.21         1.58         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.43         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
        5.19         6.87        75.25        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        61.41        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
        3.06         2.14         0.07         1.35       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       48.20        51.32         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 
       13.02        11.01        11.08        11.08        10.06        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32         7.92        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        4.50        17.13        16.14        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        38.20       130.65       140.38         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
       13.38        13.64        13.45         6.18        16.31        16.24 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       26.43        46.75        47.15         4.11        10.98         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        5.59        17.29         6.64        30.28        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        12.72        37.74        10.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       20.02        10.39        65.98        36.03        32.02         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 
       24.00         1.02        46.03         6.05         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        7.99         1.02        32.98         1.02        36.95         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        0.99        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
        1.02        31.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.05         9.37         4.73        60.03         7.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06       126.44        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
        0.49        17.00        15.85        16.34        16.31        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       10.78        13.64         9.96        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.02         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK  9(8Q12.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
       37.02        46.65        23.38        42.28        44.91        37.05 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       34.65        14.53        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.06        22.52         8.38        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        52.44 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 
        1.02         3.02        58.03        63.98        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       34.03         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 
       19.99        13.94        61.02         2.01         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        19.00        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 
        0.99        36.03        32.05        31.07        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       33.01        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       50.99        13.05        25.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       42.02        14.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       32.02        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        39.98         2.01 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 
        0.79         0.72         1.02         0.76         0.46        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        15.75        17.82         5.52        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 
        1.41         5.65         6.77       100.01         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.14         2.93       124.27        23.05        26.04 
TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       22.03        12.00        16.04        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 
       13.05        11.01        12.03        14.99        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 
       17.75        18.25        17.85        12.49        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.64         1.51        12.00        24.43        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 
       14.04        26.47        81.37       119.93        95.18        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        29.59        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 
       35.41        19.43       107.67        28.21        82.39        51.75 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 
       91.79        52.80        10.52         2.79         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
        5.49        26.99        14.76        13.55        19.10        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
        8.45        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         2.01        34.03         2.01        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99         0.99        29.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 
       19.99        17.03        13.02        35.01        14.01        19.99 
TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A01L 
       36.03        20.98        13.94         6.02        36.03        12.00 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 
       10.98        49.97        38.96        41.00         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.05         6.97        13.97        10.98        11.01        15.02 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       30.05        12.95         5.29       129.27        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-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       16.41         8.61        17.46        11.97         8.45        31.30 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.66         0.69         0.53         1.12 

  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                       16.340                        19.265 
[1] "0.1 - 140.4 (16.3)" "0.1 - 139.2 (19.3)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   232  93
  AMP PEAK  9(8Q12.1) WILD-TYPE 206  69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    232   93
  AMP PEAK  9(8Q12.1) WILD-TYPE  206   69
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON                          232                           206
  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        86         4
  AMP PEAK  9(8Q12.1) WILD-TYPE      54        1       14        85         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(8Q12.1) MUTATED           3        11         12         43
  AMP PEAK  9(8Q12.1) WILD-TYPE         0        15          9         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q12.1) MUTATED           32       43        14         0
  AMP PEAK  9(8Q12.1) WILD-TYPE         21       18        13         2
D9V4, multiclass
            clus
vv           AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  STAGE I                             48                            54
  STAGE IA                             0                             1
  STAGE II                            22                            14
  STAGE IIA                           86                            85
  STAGE IIB                            4                             6
  STAGE IIC                            3                             0
  STAGE III                           11                            15
  STAGE IIIA                          12                             9
  STAGE IIIB                          43                            35
  STAGE IIIC                          32                            21
  STAGE IV                            43                            18
  STAGE IVA                           14                            13
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(8Q12.1) MUTATED     7  54 227  36
  AMP PEAK  9(8Q12.1) WILD-TYPE  13  51 185  29
D9V5, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  T1                           7                            13
  T2                          54                            51
  T3                         227                           185
  T4                          36                            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  9(8Q12.1) MUTATED   174  78  70
  AMP PEAK  9(8Q12.1) WILD-TYPE 167  70  42
D9V6, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  N0                         174                           167
  N1                          78                            70
  N2                          70                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  9(8Q12.1) MUTATED   226  49   8   0  38
  AMP PEAK  9(8Q12.1) WILD-TYPE 220  25   2   2  25
D9V7, multiclass
     clus
vv    AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  M0                          226                           220
  M1                           49                            25
  M1A                           8                             2
  M1B                           0                             2
  MX                           38                            25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   147 178
  AMP PEAK  9(8Q12.1) WILD-TYPE 136 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    147  178
  AMP PEAK  9(8Q12.1) WILD-TYPE  136  143
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  FEMALE                         147                           136
  MALE                           178                           143
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                    209
  AMP PEAK  9(8Q12.1) WILD-TYPE                  169
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                              23
  AMP PEAK  9(8Q12.1) WILD-TYPE                            36
                               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
D9V9, multiclass
                                clus
vv                               AMP PEAK  9(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   209
  COLON MUCINOUS ADENOCARCINOMA                           23
  RECTAL ADENOCARCINOMA                                   87
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     169
  COLON MUCINOUS ADENOCARCINOMA                             36
  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"
D9V10, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED     8 317
  AMP PEAK  9(8Q12.1) WILD-TYPE   1 278
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED      8  317
  AMP PEAK  9(8Q12.1) WILD-TYPE    1  278
     clus
vv    AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  NO                            8                             1
  YES                         317                           278
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(8Q12.1) MUTATED   224   3  26  17
  AMP PEAK  9(8Q12.1) WILD-TYPE 212   2  10  12
D9V11, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  R0                         224                           212
  R1                           3                             2
  R2                          26                            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                          31   169
  AMP PEAK  9(8Q12.1) WILD-TYPE                        25   123
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 31
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK  9(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(8Q24.21) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(8Q24.21) MUTATED   276  68
  AMP PEAK 10(8Q24.21) WILD-TYPE 190  41
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           344                            231 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                            68                             41 
$`AMP PEAK 10(8Q24.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        31.63        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       23.61        32.71        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        20.61        24.69        23.87        20.28 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 
       35.01         6.97         1.02        24.03        36.03        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 
       33.99        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05         6.97        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
       85.05        19.04         0.99         0.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        33.07        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       24.00        20.98        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       26.01        24.00        27.02        13.94        19.00        18.05 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        21.99        15.02         0.99        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       31.00         1.02        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        5.03         0.92        41.00         0.07        21.37         4.21 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        1.58         1.02         0.10         0.20         0.43         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.09        16.31         0.20        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        61.41        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.10         1.35       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       15.62        48.20        51.32        21.99         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 
       14.99        12.99        13.02        11.08        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F 
       49.91       140.38         7.50        44.32         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 
       13.45         6.18        16.31        16.24         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       45.11        39.42        35.93        36.00        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YX 
       47.15         4.11        10.98         5.59         5.49        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        6.64        30.28        67.00        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 
       43.04        13.55        12.72        37.74        10.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       10.39        86.63        65.98        36.03        32.02         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       24.00         1.02        46.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
        0.99         1.02        36.95        17.03         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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       17.03         0.99        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
        0.69         0.72        10.19         6.05         9.37         4.73 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        36.00         7.10        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
        2.40        17.00        15.85        16.34        16.31        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       10.78        13.64         9.96        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        1.02         0.53         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 10(8Q24.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-4105 
       46.65        23.38        42.28        44.91        37.05        14.53 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        22.52         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       61.84         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       38.99         1.02         9.07        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       34.03        21.01        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 
       61.02         2.01         0.92        47.05        11.01        19.00 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 
       15.95        38.99        14.93         0.99        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       53.00        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       21.99        50.99        13.05        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       27.02        38.04        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C 
        4.01        27.02        42.02        14.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       32.02        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y 
       35.01        26.01        39.06        39.98        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       18.05        40.96        56.55         0.79         0.72         0.76 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        15.75        17.82         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 
       50.37        58.39         1.41         6.77       100.01         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 
        0.26         0.33        17.56        40.34        70.16        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 
        2.93       124.27        23.05        26.04        22.03        12.00 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       16.04        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 
       11.08        11.01        12.03        14.99        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       18.25        17.85        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       12.00        92.75        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2693 
        5.98         1.32         5.19        26.99        14.76        19.10 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
       14.50         8.45        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         2.01        34.03        12.03        15.95        19.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       29.98         0.99        19.99        13.02        35.01        14.01 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 
       20.98        13.94         6.02        36.03        12.00        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
       49.97        38.96         4.60         1.81         6.05         6.97 
TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE 
       13.97        15.02        30.05        12.95         5.29       129.27 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
       51.48        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       16.41         8.61        17.46        11.97         8.45        31.30 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
        0.66         0.69         1.12 

  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                          0.07                           0.26 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                         17.03                          19.00 
[1] "0.1 - 140.4 (17.0)" "0.3 - 139.2 (19.0)"
[1] "hr=" "1.2"
D10V2, continuous
D10V3, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   254 107
  AMP PEAK 10(8Q24.21) WILD-TYPE 184  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    254  107
  AMP PEAK 10(8Q24.21) WILD-TYPE  184   55
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON                           254                            184
  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        97         4
  AMP PEAK 10(8Q24.21) WILD-TYPE      46        1       12        74         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(8Q24.21) MUTATED           3        13         15         47
  AMP PEAK 10(8Q24.21) WILD-TYPE         0        13          6         31
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(8Q24.21) MUTATED           33       46        16         0
  AMP PEAK 10(8Q24.21) WILD-TYPE         20       15        11         2
D10V4, multiclass
            clus
vv           AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  STAGE I                              56                             46
  STAGE IA                              0                              1
  STAGE II                             24                             12
  STAGE IIA                            97                             74
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            13                             13
  STAGE IIIA                           15                              6
  STAGE IIIB                           47                             31
  STAGE IIIC                           33                             20
  STAGE IV                             46                             15
  STAGE IVA                            16                             11
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 10(8Q24.21) MUTATED     8  64 252  37
  AMP PEAK 10(8Q24.21) WILD-TYPE  12  41 160  28
D10V5, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  T1                            8                             12
  T2                           64                             41
  T3                          252                            160
  T4                           37                             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 10(8Q24.21) MUTATED   198  85  76
  AMP PEAK 10(8Q24.21) WILD-TYPE 143  63  36
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  N0                          198                            143
  N1                           85                             63
  N2                           76                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 10(8Q24.21) MUTATED   257  54   8   0  39
  AMP PEAK 10(8Q24.21) WILD-TYPE 189  20   2   2  24
D10V7, multiclass
     clus
vv    AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  M0                           257                            189
  M1                            54                             20
  M1A                            8                              2
  M1B                            0                              2
  MX                            39                             24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   162 200
  AMP PEAK 10(8Q24.21) WILD-TYPE 121 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    162  200
  AMP PEAK 10(8Q24.21) WILD-TYPE  121  121
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  FEMALE                          162                            121
  MALE                            200                            121
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                    225
  AMP PEAK 10(8Q24.21) WILD-TYPE                  153
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                              28
  AMP PEAK 10(8Q24.21) WILD-TYPE                            31
                                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
D10V9, multiclass
                                clus
vv                               AMP PEAK 10(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                    225
  COLON MUCINOUS ADENOCARCINOMA                            28
  RECTAL ADENOCARCINOMA                                   100
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      153
  COLON MUCINOUS ADENOCARCINOMA                              31
  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"
D10V10, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED     8 354
  AMP PEAK 10(8Q24.21) WILD-TYPE   1 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED      8  354
  AMP PEAK 10(8Q24.21) WILD-TYPE    1  241
     clus
vv    AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  NO                             8                              1
  YES                          354                            241
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(8Q24.21) MUTATED   252   3  27  19
  AMP PEAK 10(8Q24.21) WILD-TYPE 184   2   9  10
D10V11, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  R0                          252                            184
  R1                            3                              2
  R2                           27                              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                          34   184
  AMP PEAK 10(8Q24.21) WILD-TYPE                        22   108
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  34
  WHITE                                                     184
                                  clus
vv                                 AMP PEAK 10(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(10Q22.3) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(10Q22.3) MUTATED    27   8
  AMP PEAK 11(10Q22.3) WILD-TYPE 439 101
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            35                            540 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                             8                            101 
$`AMP PEAK 11(10Q22.3) MUTATED`
TCGA-4T-AA8H TCGA-A6-6649 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3952 
        5.26        24.16         2.01        33.07        27.02         2.01 
TCGA-AA-3982 TCGA-AA-A01Q TCGA-AA-A01R TCGA-AY-A54L TCGA-CM-5860 TCGA-CM-6163 
       27.02         1.02        35.01         5.19        16.01        14.04 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.01        19.59        10.13        14.30        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 TCGA-G4-6299 TCGA-G4-6314 
      140.38         7.50       131.51         6.12        74.56        35.93 
TCGA-G4-6317 TCGA-AF-2689 TCGA-AF-A56K TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3999 
       36.00        17.95        86.63        46.03        50.04        28.04 
TCGA-AG-A01W TCGA-AG-A020 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-4745 
       70.03        10.98        10.19         6.05        10.98 

$`AMP PEAK 11(10Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        7.53        12.39        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DB 
       24.43        38.20       130.65        92.75        49.91        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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        23.51        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 
       44.68        55.04        51.75        45.11        39.42        36.72 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        47.15        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       67.00        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        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         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02        34.03         2.01        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-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-A023 TCGA-AG-A025 TCGA-AG-A026 
       12.00        31.00        64.01        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.73        13.97        60.03         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-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        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                          1.02                           0.07 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                        16.010                         17.835 
[1] "1.0 - 140.4 (16.0)" "0.1 - 139.2 (17.8)"
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    27  11
  AMP PEAK 11(10Q22.3) WILD-TYPE 411 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     27   11
  AMP PEAK 11(10Q22.3) WILD-TYPE  411  151
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON                            27                            411
  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         4        0        2         9         0
  AMP PEAK 11(10Q22.3) WILD-TYPE      98        1       34       162        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         19         74
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(10Q22.3) MUTATED            6        5         1         0
  AMP PEAK 11(10Q22.3) WILD-TYPE         47       56        26         2
D11V4, multiclass
            clus
vv           AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  STAGE I                               4                             98
  STAGE IA                              0                              1
  STAGE II                              2                             34
  STAGE IIA                             9                            162
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            2                             19
  STAGE IIIB                            4                             74
  STAGE IIIC                            6                             47
  STAGE IV                              5                             56
  STAGE IVA                             1                             26
  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   3  32   2
  AMP PEAK 11(10Q22.3) WILD-TYPE  19 102 380  63
D11V5, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  T1                            1                             19
  T2                            3                            102
  T3                           32                            380
  T4                            2                             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
  AMP PEAK 11(10Q22.3) MUTATED    15  11  12
  AMP PEAK 11(10Q22.3) WILD-TYPE 326 137 100
D11V6, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  N0                           15                            326
  N1                           11                            137
  N2                           12                            100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 11(10Q22.3) MUTATED    27   5   1   0   3
  AMP PEAK 11(10Q22.3) WILD-TYPE 419  69   9   2  60
D11V7, multiclass
     clus
vv    AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  M0                            27                            419
  M1                             5                             69
  M1A                            1                              9
  M1B                            0                              2
  MX                             3                             60
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    16  22
  AMP PEAK 11(10Q22.3) WILD-TYPE 267 299
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     16   22
  AMP PEAK 11(10Q22.3) WILD-TYPE  267  299
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  FEMALE                           16                            267
  MALE                             22                            299
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                     23
  AMP PEAK 11(10Q22.3) WILD-TYPE                  355
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                               4
  AMP PEAK 11(10Q22.3) WILD-TYPE                            55
                                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
D11V9, multiclass
                                clus
vv                               AMP PEAK 11(10Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     23
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      355
  COLON MUCINOUS ADENOCARCINOMA                              55
  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"
D11V10, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED     1  37
  AMP PEAK 11(10Q22.3) WILD-TYPE   8 558
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED      1   37
  AMP PEAK 11(10Q22.3) WILD-TYPE    8  558
     clus
vv    AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  NO                             1                              8
  YES                           37                            558
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(10Q22.3) MUTATED    26   0   1   1
  AMP PEAK 11(10Q22.3) WILD-TYPE 410   5  35  28
D11V11, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  R0                           26                            410
  R1                            0                              5
  R2                            1                             35
  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                           3    21
  AMP PEAK 11(10Q22.3) WILD-TYPE                        53   271
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(10Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      21
                                  clus
vv                                 AMP PEAK 11(10Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    53
  WHITE                                                       271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(11P15.5) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(11P15.5) MUTATED   104  24
  AMP PEAK 12(11P15.5) WILD-TYPE 362  85
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           128                            447 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                            24                             85 
$`AMP PEAK 12(11P15.5) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
       37.02        43.43        17.79        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3506 
       25.18        23.87         9.63         5.03         1.02        58.03 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3542 
        9.07        24.03        19.07        34.03        29.00        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 
       13.02        24.00        23.01        13.94        19.99        50.04 
TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3846 
       47.01         5.03        25.02        17.98        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 
       33.07         0.99        24.03        18.05        20.98        27.02 
TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S 
       19.07        34.03        17.03        21.99         0.99         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6888 TCGA-AD-6901 
       35.01        26.01        39.98         5.03         4.21         1.02 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 
        0.46        16.31         0.95         6.87        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
       29.56         3.19         1.94         2.14         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 
        1.35       102.44         8.02        30.08        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6536 
       21.99        11.08        12.26        13.51         1.32        17.85 
TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 
        7.53        13.41        49.91        35.97        60.79        13.38 
TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       13.64         8.35        74.56        61.87        55.04        45.11 
TCGA-G4-6314 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       35.93        26.99        30.28        17.95        17.23        13.55 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       10.39         8.45        20.02        10.39        65.98        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 
       12.00         8.02         2.01        46.03        34.03        19.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H 
       19.99         0.99        14.01        36.03         1.02        25.97 
TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4749 
       31.00         4.60        10.19         9.37        13.97        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       15.02        12.99        12.00        36.00        30.05       126.44 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6811 
        0.49         2.40        20.55        16.31         0.39         1.02 
TCGA-F5-6861 TCGA-G5-6233 
        1.12        18.28 

$`AMP PEAK 12(11P15.5) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.16        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
        1.02         3.02        37.05         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3522 
        6.97         1.02        13.02        38.99         1.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 
       36.03         8.05        19.07        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       19.04         0.99         0.99        35.05         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 
       15.95        38.99        36.95        14.93         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       24.00         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       42.02         0.99        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        33.04        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        1.58         0.10         0.76         0.20         0.43         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        5.65        32.94         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        19.59        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25         7.92        15.12         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37       119.93       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
       19.43       107.67        28.21        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        39.42        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        47.15        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
        5.49        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       43.04        19.10        12.72        37.74        14.50        15.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       86.63        11.84        32.02         7.07         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       15.95         7.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04        17.03         0.99        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-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         0.72         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 
        6.97         4.73        60.03         7.99        10.98        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02         7.10        12.95        13.05        10.06         5.29 
TCGA-DY-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-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       14.86         0.66         0.69         0.53         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                        126.44                         140.38 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                         17.90                          17.75 
[1] "0.1 - 126.4 (17.9)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    89  44
  AMP PEAK 12(11P15.5) WILD-TYPE 349 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     89   44
  AMP PEAK 12(11P15.5) WILD-TYPE  349  118
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  COLON                            89                            349
  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      82        1       30       136         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(11P15.5) MUTATED           1         6          7         17
  AMP PEAK 12(11P15.5) WILD-TYPE         2        20         14         61
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(11P15.5) MUTATED           14       18         7         0
  AMP PEAK 12(11P15.5) WILD-TYPE         39       43        20         2
D12V4, multiclass
            clus
vv           AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  STAGE I                              20                             82
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            35                            136
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            7                             14
  STAGE IIIB                           17                             61
  STAGE IIIC                           14                             39
  STAGE IV                             18                             43
  STAGE IVA                             7                             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 12(11P15.5) MUTATED     6  24  96   9
  AMP PEAK 12(11P15.5) WILD-TYPE  14  81 316  56
D12V5, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  T1                            6                             14
  T2                           24                             81
  T3                           96                            316
  T4                            9                             56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 12(11P15.5) MUTATED    70  34  30
  AMP PEAK 12(11P15.5) WILD-TYPE 271 114  82
D12V6, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  N0                           70                            271
  N1                           34                            114
  N2                           30                             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 12(11P15.5) MUTATED    99  21   3   0   9
  AMP PEAK 12(11P15.5) WILD-TYPE 347  53   7   2  54
D12V7, multiclass
     clus
vv    AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  M0                            99                            347
  M1                            21                             53
  M1A                            3                              7
  M1B                            0                              2
  MX                             9                             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    65  70
  AMP PEAK 12(11P15.5) WILD-TYPE 218 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     65   70
  AMP PEAK 12(11P15.5) WILD-TYPE  218  251
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  FEMALE                           65                            218
  MALE                             70                            251
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                     85
  AMP PEAK 12(11P15.5) WILD-TYPE                  293
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                               3
  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
D12V9, multiclass
                                clus
vv                               AMP PEAK 12(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                     85
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 12(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                      293
  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"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED     4 131
  AMP PEAK 12(11P15.5) WILD-TYPE   5 464
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED      4  131
  AMP PEAK 12(11P15.5) WILD-TYPE    5  464
     clus
vv    AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  NO                             4                              5
  YES                          131                            464
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(11P15.5) MUTATED    96   1  10   7
  AMP PEAK 12(11P15.5) WILD-TYPE 340   4  26  22
D12V11, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  R0                           96                            340
  R1                            1                              4
  R2                           10                             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"
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                          10    64
  AMP PEAK 12(11P15.5) WILD-TYPE                        46   228
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      64
                                  clus
vv                                 AMP PEAK 12(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    46
  WHITE                                                       228
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(12P13.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(12P13.32) MUTATED   108  29
  AMP PEAK 13(12P13.32) WILD-TYPE 358  80
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            137                             438 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             29                              80 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 
        5.06         5.26        44.91        13.94        16.04        34.65 
TCGA-A6-4105 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 
       14.53        22.09        25.08        20.61        20.12        20.28 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3534 
       24.92         1.02        58.03        36.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 
       12.99        19.99        78.08         0.92        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       37.02        14.93        33.07        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I 
       24.00         2.01        34.03        18.05        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J 
       33.04        51.98         0.92        22.03        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 
        0.07         0.10         0.20         0.92         6.87         1.41 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        49.41         6.77        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 
        3.06       102.44        40.34        15.62        51.32        20.02 
TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 
        8.02        30.08        16.01        15.02        15.02        21.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       13.02        14.04        11.01        11.01        20.19        17.75 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 
        4.50        12.49        15.58        14.30        11.64        13.41 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB 
       12.00        10.26       119.70        24.43        13.32        44.32 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 
       95.18         8.61        35.87        16.31        44.68        35.93 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-AF-2693 TCGA-AF-3400 
       13.78        47.15        10.98         5.59        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 
       37.74        14.50         8.45        10.39        36.03        46.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3883 
        2.01         6.05        19.99         7.99         1.02         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         0.99        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        60.03        13.05        10.06 
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-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        23.61        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52        24.13         8.38        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 
       24.69        24.39        23.87        19.66        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       47.01        15.02        19.00        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       36.95        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 
       29.98        18.05        31.00         2.01        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
        1.02        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 
       39.98         2.01         5.03        41.00        18.05        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.43         0.46        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
      100.01        29.56         5.23         2.24         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        70.16        48.20        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
        2.01       124.27        23.05        37.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 
       27.02        13.02        29.06        22.03        22.98        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 
       16.04        14.99        12.99        15.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
        7.92        15.12        17.85        17.13        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       12.39        10.13        12.43         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       11.38        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 
       53.62        55.04        51.75        45.11        39.42        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        26.04        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80         4.11        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        6.64        14.76        30.28        67.00        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 
       17.23        43.04        13.55        10.39        15.39        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        65.98        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-3593 
        7.07         1.02         2.01        24.00         1.02        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 
       50.04        12.03         0.99        15.95        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 
       29.98        32.98         0.99         0.99        19.99        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         1.02        17.03        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         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97         9.37        13.97         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD 
       36.00         7.10        30.05        12.95        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 
       37.51        31.30        14.86         0.39         1.02         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         126.44                          140.38 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                          15.95                           18.05 
[1] "0.1 - 126.4 (15.9)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   109  38
  AMP PEAK 13(12P13.32) WILD-TYPE 329 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    109   38
  AMP PEAK 13(12P13.32) WILD-TYPE  329  124
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  COLON                            109                             329
  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        22        1       13        50         2
  AMP PEAK 13(12P13.32) WILD-TYPE      80        0       23       121         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(12P13.32) MUTATED           1         5          7          9
  AMP PEAK 13(12P13.32) WILD-TYPE         2        21         14         69
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(12P13.32) MUTATED           14       15         8         0
  AMP PEAK 13(12P13.32) WILD-TYPE         39       46        19         2
D13V4, multiclass
            clus
vv           AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  STAGE I                               22                              80
  STAGE IA                               1                               0
  STAGE II                              13                              23
  STAGE IIA                             50                             121
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              5                              21
  STAGE IIIA                             7                              14
  STAGE IIIB                             9                              69
  STAGE IIIC                            14                              39
  STAGE IV                              15                              46
  STAGE IVA                              8                              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 13(12P13.32) MUTATED     2  27 100  19
  AMP PEAK 13(12P13.32) WILD-TYPE  18  78 312  46
D13V5, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  T1                             2                              18
  T2                            27                              78
  T3                           100                             312
  T4                            19                              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 13(12P13.32) MUTATED    93  27  29
  AMP PEAK 13(12P13.32) WILD-TYPE 248 121  83
D13V6, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  N0                            93                             248
  N1                            27                             121
  N2                            29                              83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 13(12P13.32) MUTATED   107  15   5   0  21
  AMP PEAK 13(12P13.32) WILD-TYPE 339  59   5   2  42
D13V7, multiclass
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  M0                            107                             339
  M1                             15                              59
  M1A                             5                               5
  M1B                             0                               2
  MX                             21                              42
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    68  81
  AMP PEAK 13(12P13.32) WILD-TYPE 215 240
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     68   81
  AMP PEAK 13(12P13.32) WILD-TYPE  215  240
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            68                             215
  MALE                              81                             240
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                     96
  AMP PEAK 13(12P13.32) WILD-TYPE                  282
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                              13
  AMP PEAK 13(12P13.32) WILD-TYPE                            46
                                 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
D13V9, 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                                       282
  COLON MUCINOUS ADENOCARCINOMA                               46
  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"
D13V10, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     3 146
  AMP PEAK 13(12P13.32) WILD-TYPE   6 449
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      3  146
  AMP PEAK 13(12P13.32) WILD-TYPE    6  449
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                              3                               6
  YES                           146                             449
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 13(12P13.32) MUTATED   109   1   6   6
  AMP PEAK 13(12P13.32) WILD-TYPE 327   4  30  23
D13V11, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  R0                           109                             327
  R1                             1                               4
  R2                             6                              30
  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                          11    74
  AMP PEAK 13(12P13.32) WILD-TYPE                        45   218
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       74
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     45
  WHITE                                                        218
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(13Q12.13) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 14(13Q12.13) MUTATED   301  74
  AMP PEAK 14(13Q12.13) WILD-TYPE 165  35
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            375                             200 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                             74                              35 
$`AMP PEAK 14(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        9.63         5.03         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
        6.97        38.99         9.07        24.03        36.03        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       50.04        15.02         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 
       36.95        37.02        14.93        17.03         0.99        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       29.98         2.01        12.99        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W 
       13.94        19.00        34.03        17.03        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y 
       33.04         2.96        39.98         2.01        41.00        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        21.37         0.79         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.43        14.50        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 
       21.44         5.19         6.87        75.25        50.37         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        3.06         0.07         1.35        17.56       102.44        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       21.99         2.01        20.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.50        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        7.50       131.51         7.76         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 
      119.93        35.97         8.61        13.38         6.18        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       44.68        45.11        39.42        35.93        36.00        26.43 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       35.80        91.79        46.75        47.15         4.11        10.52 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-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-3593 TCGA-AG-3594 
        1.02         2.01         1.02        46.03        34.03         2.01 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
        0.99        19.99        19.99         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-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         0.99         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         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        12.00        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-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        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`AMP PEAK 14(13Q12.13) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 
       19.07        17.95        29.95        23.01        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
       54.02         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       26.99        19.04         1.02        17.98        15.95        38.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
       33.07        36.03        53.00        18.05        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01         2.01        25.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       21.99        34.98        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 
        5.03         0.92        22.03        18.05         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72         0.76         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        0.20        17.82         5.52        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 
       61.41         6.77       100.01         3.19         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 
        3.29         0.26         0.33         0.10        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       37.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64         1.51        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
       98.24        95.18        11.11        13.64        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
        1.55        16.31        19.43        43.07        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 
       51.75        36.72        22.09        26.04        13.78        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 
       52.80        10.98         2.79         5.98         1.32        14.76 
TCGA-WS-AB45 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       67.00        12.72        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 
       24.00        50.04        12.03         6.05        15.95         7.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
        1.02        32.98         0.99        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 
       12.95         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                            0.07 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                         17.030                          18.545 
[1] "0.1 - 131.5 (17.0)" "0.1 - 140.4 (18.5)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   266 123
  AMP PEAK 14(13Q12.13) WILD-TYPE 172  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    266  123
  AMP PEAK 14(13Q12.13) WILD-TYPE  172   39
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  COLON                            266                             172
  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        63        0       16        98         4
  AMP PEAK 14(13Q12.13) WILD-TYPE      39        1       20        73         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(13Q12.13) MUTATED           3        15         17         58
  AMP PEAK 14(13Q12.13) WILD-TYPE         0        11          4         20
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(13Q12.13) MUTATED           38       50        23         0
  AMP PEAK 14(13Q12.13) WILD-TYPE         15       11         4         2
D14V4, multiclass
            clus
vv           AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  STAGE I                               63                              39
  STAGE IA                               0                               1
  STAGE II                              16                              20
  STAGE IIA                             98                              73
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             15                              11
  STAGE IIIA                            17                               4
  STAGE IIIB                            58                              20
  STAGE IIIC                            38                              15
  STAGE IV                              50                              11
  STAGE IVA                             23                               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  64 271  43
  AMP PEAK 14(13Q12.13) WILD-TYPE   6  41 141  22
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  T1                            14                               6
  T2                            64                              41
  T3                           271                             141
  T4                            43                              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   194 112  85
  AMP PEAK 14(13Q12.13) WILD-TYPE 147  36  27
D14V6, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  N0                           194                             147
  N1                           112                              36
  N2                            85                              27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 14(13Q12.13) MUTATED   279  61   8   0  41
  AMP PEAK 14(13Q12.13) WILD-TYPE 167  13   2   2  22
D14V7, multiclass
     clus
vv    AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  M0                            279                             167
  M1                             61                              13
  M1A                             8                               2
  M1B                             0                               2
  MX                             41                              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   181 212
  AMP PEAK 14(13Q12.13) WILD-TYPE 102 109
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    181  212
  AMP PEAK 14(13Q12.13) WILD-TYPE  102  109
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  FEMALE                           181                             102
  MALE                             212                             109
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                    249
  AMP PEAK 14(13Q12.13) WILD-TYPE                  129
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                              17
  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
D14V9, multiclass
                                clus
vv                               AMP PEAK 14(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                     249
  COLON MUCINOUS ADENOCARCINOMA                             17
  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"
D14V10, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED     7 386
  AMP PEAK 14(13Q12.13) WILD-TYPE   2 209
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED      7  386
  AMP PEAK 14(13Q12.13) WILD-TYPE    2  209
     clus
vv    AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  NO                              7                               2
  YES                           386                             209
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 14(13Q12.13) MUTATED   279   3  28  13
  AMP PEAK 14(13Q12.13) WILD-TYPE 157   2   8  16
D14V11, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  R0                           279                             157
  R1                             3                               2
  R2                            28                               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                          36   204
  AMP PEAK 14(13Q12.13) WILD-TYPE                        20    88
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      204
                                  clus
vv                                 AMP PEAK 14(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                         88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(13Q12.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(13Q12.2) MUTATED   298  72
  AMP PEAK 15(13Q12.2) WILD-TYPE 168  37
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           370                            205 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                            72                             37 
$`AMP PEAK 15(13Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        9.63         5.03         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
        6.97        38.99         9.07        24.03        36.03        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       50.04        15.02         5.98        37.05        19.00        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 
        0.99         0.99        35.05         0.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03         0.99        32.05         0.99        31.07 
TCGA-AA-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-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       12.99        24.00        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 
       16.08        50.99        13.05        34.06        26.01        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        42.02        14.99        15.02        15.02         0.99 
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 
        1.58         1.02         0.10         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        15.75        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25        50.37         1.41         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 
       11.74         1.94         2.24         3.06         0.07         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       17.56       102.44        48.20        21.99         2.01        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01         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 
       14.04        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        13.51        11.51        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32         7.92        15.12        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 
       13.41        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 
       13.38         6.18        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       23.51        61.87        44.68        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        35.80        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        4.11        10.52         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        30.28        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-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-3593 
        7.07         1.02         2.01         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
        2.01         0.99        19.99        19.99         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03         0.99         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 
        0.49         0.69         0.72         4.60         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        30.05        13.05        10.06       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        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39         1.02         0.66         0.69         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK 15(13Q12.2) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 
       19.07        17.95        29.95        23.01        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
       54.02         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99        19.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 
       15.95        38.99        33.07        36.03        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       31.00        33.01        24.00         2.01         2.01        25.02 
TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       24.00        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K 
       27.02         0.99        17.03        21.99        34.98        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.06        51.98         5.03         0.92        22.03 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07         4.21        56.55         0.72         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
        0.46         0.92        27.09         0.20        17.82         5.52 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         5.65        32.94        61.41         6.77       100.01 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.19         2.14         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.10        40.34        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
        2.93       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 
       15.02        15.02        12.00        21.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 
       13.05        12.03        14.99        20.19        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD 
       15.58        12.39         9.44        11.64         1.51        24.43 
TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       38.20        12.59       140.38        44.32       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       81.37        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 
       13.64        13.45        35.87         1.55        16.31        19.43 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       74.56        43.07        53.62        55.04        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U 
       22.09        26.04        13.78        26.17        52.80        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 
        2.79         5.98         1.32        14.76        67.00        12.72 
TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 
        8.45        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         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 
       32.98         0.99        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         6.05        13.97        12.95 
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                           0.07 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                         17.08                          18.05 
[1] "0.1 - 131.5 (17.1)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   262 122
  AMP PEAK 15(13Q12.2) WILD-TYPE 176  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    262  122
  AMP PEAK 15(13Q12.2) WILD-TYPE  176   40
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  COLON                           262                            176
  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        63        0       16        96         4
  AMP PEAK 15(13Q12.2) WILD-TYPE      39        1       20        75         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(13Q12.2) MUTATED           3        15         17         58
  AMP PEAK 15(13Q12.2) WILD-TYPE         0        11          4         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(13Q12.2) MUTATED           37       49        22         0
  AMP PEAK 15(13Q12.2) WILD-TYPE         16       12         5         2
D15V4, multiclass
            clus
vv           AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  STAGE I                              63                             39
  STAGE IA                              0                              1
  STAGE II                             16                             20
  STAGE IIA                            96                             75
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            15                             11
  STAGE IIIA                           17                              4
  STAGE IIIB                           58                             20
  STAGE IIIC                           37                             16
  STAGE IV                             49                             12
  STAGE IVA                            22                              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  64 266  43
  AMP PEAK 15(13Q12.2) WILD-TYPE   6  41 146  22
D15V5, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  T1                           14                              6
  T2                           64                             41
  T3                          266                            146
  T4                           43                             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   192 110  84
  AMP PEAK 15(13Q12.2) WILD-TYPE 149  38  28
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  N0                          192                            149
  N1                          110                             38
  N2                           84                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 15(13Q12.2) MUTATED   276  59   8   0  41
  AMP PEAK 15(13Q12.2) WILD-TYPE 170  15   2   2  22
D15V7, multiclass
     clus
vv    AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  M0                           276                            170
  M1                            59                             15
  M1A                            8                              2
  M1B                            0                              2
  MX                            41                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   177 211
  AMP PEAK 15(13Q12.2) WILD-TYPE 106 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    177  211
  AMP PEAK 15(13Q12.2) WILD-TYPE  106  110
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  FEMALE                          177                            106
  MALE                            211                            110
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                    245
  AMP PEAK 15(13Q12.2) WILD-TYPE                  133
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                              17
  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
D15V9, multiclass
                                clus
vv                               AMP PEAK 15(13Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    245
  COLON MUCINOUS ADENOCARCINOMA                            17
  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"
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED     7 381
  AMP PEAK 15(13Q12.2) WILD-TYPE   2 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED      7  381
  AMP PEAK 15(13Q12.2) WILD-TYPE    2  214
     clus
vv    AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  NO                             7                              2
  YES                          381                            214
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(13Q12.2) MUTATED   276   3  27  13
  AMP PEAK 15(13Q12.2) WILD-TYPE 160   2   9  16
D15V11, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  R0                          276                            160
  R1                            3                              2
  R2                           27                              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                          36   201
  AMP PEAK 15(13Q12.2) WILD-TYPE                        20    91
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 15(13Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                        91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(13Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(13Q22.1) MUTATED   301  73
  AMP PEAK 16(13Q22.1) WILD-TYPE 165  36
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           374                            201 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            73                             36 
$`AMP PEAK 16(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        9.63         5.03         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
        6.97        38.99         9.07        24.03        36.03        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       50.04        15.02         5.98        37.05        19.00        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 
        0.99         0.99        35.05         0.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03         0.99        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       34.03        17.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S 
       15.02         0.99        32.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y 
       33.04         2.96        39.98         2.01        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        1.58         1.02         0.10         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        15.75        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25        50.37         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        1.94         2.24         3.06         0.07         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
      102.44        48.20        21.99         2.01        20.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       16.01         5.03        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32         7.50       131.51 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
        7.76         6.12        14.04        26.47       119.93        35.97 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       13.38         6.18        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       23.51        74.56        61.87        44.68        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.00        26.43        35.80        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       47.15         4.11        10.52         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 
        5.49        26.99        17.29         6.64        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39        14.50        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        11.84         7.07         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 
       46.03        34.03         0.99        19.99        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       29.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03         0.99         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04         0.49         0.69         0.72         4.60         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       32.61         0.49        20.55        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        1.02         0.66         0.69         0.76        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 16(13Q22.1) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
       19.07        33.99        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
        6.97         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99        19.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       15.95        38.99        33.07        36.03        31.07        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 
       31.00        33.01        24.00         2.01        25.02        24.00 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        21.99        34.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
        5.03         0.92        22.03        18.05        56.55         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
        0.46         0.92        27.09         0.20        17.82         5.52 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        83.80        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
      100.01         3.19         2.14         3.25         3.29         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.33         0.10        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.14         2.93       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       27.02        15.02        15.02        12.00        21.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       12.95        13.05        12.03        14.99        20.19        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        15.58        12.39         9.44        11.64         1.51 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38        44.32       135.65       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 
       13.64        13.45        35.87         1.55        16.31        19.43 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       43.07        53.62        55.04        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        26.17        52.80        10.98         2.79 
TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
        1.32        14.76        67.00        12.72         8.45        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         1.02        32.98 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
        0.99        13.02        48.03        20.98        13.94        37.02 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
        1.02        31.00        10.98        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 
        1.81        10.19         6.05        13.97        12.95         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       19.96        20.91         8.61        13.64        17.46         8.45 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        0.53         1.12         0.46 

  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                         17.03                          19.07 
[1] "0.1 - 131.5 (17.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   270 117
  AMP PEAK 16(13Q22.1) WILD-TYPE 168  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    270  117
  AMP PEAK 16(13Q22.1) WILD-TYPE  168   45
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON                           270                            168
  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        64        0       20        93         4
  AMP PEAK 16(13Q22.1) WILD-TYPE      38        1       16        78         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(13Q22.1) MUTATED           3        16         17         57
  AMP PEAK 16(13Q22.1) WILD-TYPE         0        10          4         21
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(13Q22.1) MUTATED           39       48        21         0
  AMP PEAK 16(13Q22.1) WILD-TYPE         14       13         6         2
D16V4, multiclass
            clus
vv           AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  STAGE I                              64                             38
  STAGE IA                              0                              1
  STAGE II                             20                             16
  STAGE IIA                            93                             78
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           17                              4
  STAGE IIIB                           57                             21
  STAGE IIIC                           39                             14
  STAGE IV                             48                             13
  STAGE IVA                            21                              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  65 267  43
  AMP PEAK 16(13Q22.1) WILD-TYPE   5  40 145  22
D16V5, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  T1                           15                              5
  T2                           65                             40
  T3                          267                            145
  T4                           43                             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   194 111  83
  AMP PEAK 16(13Q22.1) WILD-TYPE 147  37  29
D16V6, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  N0                          194                            147
  N1                          111                             37
  N2                           83                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 16(13Q22.1) MUTATED   277  58   8   0  44
  AMP PEAK 16(13Q22.1) WILD-TYPE 169  16   2   2  19
D16V7, multiclass
     clus
vv    AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  M0                           277                            169
  M1                            58                             16
  M1A                            8                              2
  M1B                            0                              2
  MX                            44                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   175 216
  AMP PEAK 16(13Q22.1) WILD-TYPE 108 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    175  216
  AMP PEAK 16(13Q22.1) WILD-TYPE  108  105
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  FEMALE                          175                            108
  MALE                            216                            105
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                    251
  AMP PEAK 16(13Q22.1) WILD-TYPE                  127
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                              19
  AMP PEAK 16(13Q22.1) WILD-TYPE                            40
                                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
D16V9, multiclass
                                clus
vv                               AMP PEAK 16(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    251
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                   112
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      127
  COLON MUCINOUS ADENOCARCINOMA                              40
  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"
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED     7 384
  AMP PEAK 16(13Q22.1) WILD-TYPE   2 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      7  384
  AMP PEAK 16(13Q22.1) WILD-TYPE    2  211
     clus
vv    AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  NO                             7                              2
  YES                          384                            211
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(13Q22.1) MUTATED   276   3  26  14
  AMP PEAK 16(13Q22.1) WILD-TYPE 160   2  10  15
D16V11, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  R0                          276                            160
  R1                            3                              2
  R2                           26                             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                          37   201
  AMP PEAK 16(13Q22.1) WILD-TYPE                        19    91
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 16(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                        91
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(15Q26.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(15Q26.1) MUTATED    30  10
  AMP PEAK 17(15Q26.1) WILD-TYPE 436  99
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            40                            535 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            10                             99 
$`AMP PEAK 17(15Q26.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-6649 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3560 
        5.06        37.02        24.16        29.00        29.00        19.99 
TCGA-AA-3681 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 TCGA-AA-A02H TCGA-AY-4070 
        5.98        36.03         0.99        24.00         2.01        16.31 
TCGA-AY-6196 TCGA-AZ-4614 TCGA-CA-5254 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-6161 
        0.20         5.65         2.24        22.98        30.08        15.02 
TCGA-D5-6531 TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-G4-6297 
       17.75        17.13        44.32        14.04        26.47        82.39 
TCGA-G4-6299 TCGA-G4-6626 TCGA-QG-A5YV TCGA-AF-3400 TCGA-AG-3587 TCGA-AG-3609 
       74.56        46.75        26.99        12.72        46.03        19.99 
TCGA-AG-3612 TCGA-AG-A01W TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5918 
       19.99        70.03         0.69        10.19         9.37         7.99 
TCGA-DY-A1DC TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6864 
       41.36         8.45         9.96         0.46 

$`AMP PEAK 17(15Q26.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 
        8.05        19.07        19.07        34.03        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-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-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J 
       37.02        39.06        51.98         2.96        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82         5.19         5.52         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        20.42        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17         6.12        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       17.29         6.64        14.76        30.28        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-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         1.02         2.01        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.05         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       11.51        10.78        13.64        17.46        11.97        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                          0.20                           0.07 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                         82.39                         140.38 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                         18.87                          17.82 
[1] "0.2 - 82.4 (18.9)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1.4"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    29  13
  AMP PEAK 17(15Q26.1) WILD-TYPE 409 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     29   13
  AMP PEAK 17(15Q26.1) WILD-TYPE  409  149
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  COLON                            29                            409
  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      97        1       35       160        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(15Q26.1) MUTATED           0         1          0          5
  AMP PEAK 17(15Q26.1) WILD-TYPE         3        25         21         73
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(15Q26.1) MUTATED           11        5         3         0
  AMP PEAK 17(15Q26.1) WILD-TYPE         42       56        24         2
D17V4, multiclass
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  STAGE I                               5                             97
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            11                            160
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             1                             25
  STAGE IIIA                            0                             21
  STAGE IIIB                            5                             73
  STAGE IIIC                           11                             42
  STAGE IV                              5                             56
  STAGE IVA                             3                             24
  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  19 101 382  58
D17V5, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1                            1                             19
  T2                            4                            101
  T3                           30                            382
  T4                            7                             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 17(15Q26.1) MUTATED    17   8  17
  AMP PEAK 17(15Q26.1) WILD-TYPE 324 140  95
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  N0                           17                            324
  N1                            8                            140
  N2                           17                             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 17(15Q26.1) MUTATED    31   6   1   0   2
  AMP PEAK 17(15Q26.1) WILD-TYPE 415  68   9   2  61
D17V7, multiclass
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  M0                            31                            415
  M1                             6                             68
  M1A                            1                              9
  M1B                            0                              2
  MX                             2                             61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    24  18
  AMP PEAK 17(15Q26.1) WILD-TYPE 259 303
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     24   18
  AMP PEAK 17(15Q26.1) WILD-TYPE  259  303
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  FEMALE                           24                            259
  MALE                             18                            303
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                     25
  AMP PEAK 17(15Q26.1) WILD-TYPE                  353
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                               4
  AMP PEAK 17(15Q26.1) WILD-TYPE                            55
                                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
D17V9, 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                                      353
  COLON MUCINOUS ADENOCARCINOMA                              55
  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"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED     2  40
  AMP PEAK 17(15Q26.1) WILD-TYPE   7 555
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      2   40
  AMP PEAK 17(15Q26.1) WILD-TYPE    7  555
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NO                             2                              7
  YES                           40                            555
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(15Q26.1) MUTATED    30   1   3   2
  AMP PEAK 17(15Q26.1) WILD-TYPE 406   4  33  27
D17V11, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  R0                           30                            406
  R1                            1                              4
  R2                            3                             33
  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                        53   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                                    53
  WHITE                                                       268
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(16P11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(16P11.2) MUTATED   131  27
  AMP PEAK 18(16P11.2) WILD-TYPE 335  82
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           158                            417 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            27                             82 
$`AMP PEAK 18(16P11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       15.52        37.25        32.45        30.44        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       24.13        25.08        20.61        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       12.99        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3842 
       50.04        15.02        19.00        35.05        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       14.93        17.03        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98         2.01        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 
        2.01        20.98        34.03        16.08        26.01        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 
       40.96         1.02         0.10         0.20         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 
        0.20         5.19         6.87         5.13        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
        5.23         1.94         2.24         3.29         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
       48.20        21.99        20.02         8.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       22.98        16.01        17.03        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 
       14.99        15.02        11.01        10.06        19.59        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 
        1.32        15.12        17.13        12.49        10.13        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 
       11.38        38.20        13.32        35.97         8.61        13.38 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        1.55        82.39        74.56        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 
       45.11        39.42        35.93        26.43        13.78        46.75 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
        5.59         1.32        17.95        37.74        10.39        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3726 
       20.02        86.63        65.98         1.02         6.05         7.99 
TCGA-AG-3731 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
        1.02        17.03        19.99        36.03         1.02         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G 
       15.95        36.03         9.07        12.00        31.00        38.96 
TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       38.04         0.72        10.19         6.97         9.37        60.03 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG 
       11.01        12.99        12.00        10.06        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
        0.49        17.69        16.31        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6863 
        1.02         0.76 

$`AMP PEAK 18(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        16.04        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        29.00         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       21.01        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       15.95        38.99         0.99        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        18.05        31.00        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         1.58         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 
       37.02         8.02        26.04        27.02        29.06        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       16.04        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        14.99        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       13.51        11.51        20.19        20.42        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        16.14        15.58         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 
       19.43       107.67        28.21         8.35        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       53.62        51.75        36.72        36.00        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        10.52         2.79         5.98         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        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         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99        19.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       35.01        14.01         1.02        48.03        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       23.01        37.02         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.97         1.94        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         4.60         1.81         6.05         6.05 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
        4.73        13.97         7.99        10.98        15.02        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24       129.27        32.61 
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-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        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-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                         17.87                          17.82 
[1] "0.1 - 102.4 (17.9)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   121  47
  AMP PEAK 18(16P11.2) WILD-TYPE 317 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    121   47
  AMP PEAK 18(16P11.2) WILD-TYPE  317  115
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  COLON                           121                            317
  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        19        1        4        37         3
  AMP PEAK 18(16P11.2) WILD-TYPE      83        0       32       134         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(16P11.2) MUTATED           0         6         10         31
  AMP PEAK 18(16P11.2) WILD-TYPE         3        20         11         47
                                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         32       38        19         1
D18V4, multiclass
            clus
vv           AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              1                              0
  STAGE II                              4                             32
  STAGE IIA                            37                            134
  STAGE IIB                             3                              7
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                           10                             11
  STAGE IIIB                           31                             47
  STAGE IIIC                           21                             32
  STAGE IV                             23                             38
  STAGE IVA                             8                             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
  AMP PEAK 18(16P11.2) MUTATED     5  25 121  17
  AMP PEAK 18(16P11.2) WILD-TYPE  15  80 291  48
D18V5, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  T1                            5                             15
  T2                           25                             80
  T3                          121                            291
  T4                           17                             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 18(16P11.2) MUTATED    70  55  43
  AMP PEAK 18(16P11.2) WILD-TYPE 271  93  69
D18V6, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  N0                           70                            271
  N1                           55                             93
  N2                           43                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 18(16P11.2) MUTATED   114  28   3   1  19
  AMP PEAK 18(16P11.2) WILD-TYPE 332  46   7   1  44
D18V7, multiclass
     clus
vv    AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  M0                           114                            332
  M1                            28                             46
  M1A                            3                              7
  M1B                            1                              1
  MX                            19                             44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED    80  89
  AMP PEAK 18(16P11.2) WILD-TYPE 203 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED     80   89
  AMP PEAK 18(16P11.2) WILD-TYPE  203  232
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  FEMALE                           80                            203
  MALE                             89                            232
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                    113
  AMP PEAK 18(16P11.2) WILD-TYPE                  265
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                               8
  AMP PEAK 18(16P11.2) WILD-TYPE                            51
                                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
D18V9, multiclass
                                clus
vv                               AMP PEAK 18(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                    113
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 18(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      265
  COLON MUCINOUS ADENOCARCINOMA                              51
  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"
D18V10, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED     4 165
  AMP PEAK 18(16P11.2) WILD-TYPE   5 430
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED      4  165
  AMP PEAK 18(16P11.2) WILD-TYPE    5  430
     clus
vv    AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  NO                             4                              5
  YES                          165                            430
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(16P11.2) MUTATED   123   0  14   7
  AMP PEAK 18(16P11.2) WILD-TYPE 313   5  22  22
D18V11, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  R0                          123                            313
  R1                            0                              5
  R2                           14                             22
  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                          16    83
  AMP PEAK 18(16P11.2) WILD-TYPE                        40   209
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK 18(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(17Q12) MUTATED   129  19
  AMP PEAK 19(17Q12) WILD-TYPE 337  90
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         148                          427 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          19                           90 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 
        5.06         5.26        43.76        43.43        17.79        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       36.53        14.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 
       27.09        25.08        25.18        24.69        20.28         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3524 TCGA-AA-3532 
       37.05         1.02        58.03        38.99        36.03        29.00 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 
       12.99        24.00        23.01        15.02        36.00        85.05 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3869 
       35.05         1.02        17.03         0.99        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 
       18.05        12.99        34.03         2.01        50.99        13.05 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01F TCGA-AA-A01G 
       27.02        27.02        17.03        21.99        32.02        12.00 
TCGA-AA-A01S TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 
        1.02         0.92        41.00         4.21         0.79         0.10 
TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        0.43        16.31         6.87        61.41        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 
        3.19         2.24         0.07         1.35       102.44         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        29.06        22.03        17.03        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 
       21.99        14.99        13.05        11.08        11.01        19.59 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       11.51        18.25         1.32        15.12         4.50        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A285 
       14.30        13.41        24.43        38.20       130.65         6.12 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       95.18         1.55        74.56        61.87        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB 
       39.42        35.93        36.00        26.43        46.75         5.59 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L 
        5.19        17.29        30.28        17.23        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       11.84        12.00         7.07         1.02        46.03        34.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       15.95        19.99        19.99         0.99        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       48.03        32.02        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 
        9.07        31.00        64.01        51.98         0.69         4.60 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.05         9.37        12.00        13.05        10.06         5.29 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 
       51.48        17.00        18.28        16.31        11.97         1.02 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.69         0.46        55.76        26.43 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        23.38        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
        5.03        26.99        19.04         0.99         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       14.93         0.99        33.07        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        29.98        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96         0.07        21.37        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.58         1.02         0.76         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       65.00        62.79        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         3.06         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 
       20.19        20.42        17.75         7.92        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26       119.70        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        44.68        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.98         1.32 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
        5.49        26.99         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        32.02         8.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
        2.01        50.04        12.03         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3887 
        0.99        29.98         1.02        32.98         0.99        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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         0.99        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-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 
       41.00        38.04         0.49         1.45         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       10.19         6.05         6.97         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA 
       15.02        36.00         7.10        30.05        12.95       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-6511 TCGA-EI-6512 
        2.40        20.55        19.96        20.91        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.39         0.66         0.53         1.12         0.76        18.28 
TCGA-G5-6572 
       47.08 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                      130.65                       140.38 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       17.26                        17.95 
[1] "0.1 - 130.7 (17.3)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.6"
D19V2, continuous
D19V3, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   111  46
  AMP PEAK 19(17Q12) WILD-TYPE 327 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    111   46
  AMP PEAK 19(17Q12) WILD-TYPE  327  116
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  COLON                         111                          327
  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        41         1
  AMP PEAK 19(17Q12) WILD-TYPE      80        1       29       130         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(17Q12) MUTATED           1         5          5         20
  AMP PEAK 19(17Q12) WILD-TYPE         2        21         16         58
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(17Q12) MUTATED           18       24         9         1
  AMP PEAK 19(17Q12) WILD-TYPE         35       37        18         1
D19V4, multiclass
            clus
vv           AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  STAGE I                            22                           80
  STAGE IA                            0                            1
  STAGE II                            7                           29
  STAGE IIA                          41                          130
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          5                           16
  STAGE IIIB                         20                           58
  STAGE IIIC                         18                           35
  STAGE IV                           24                           37
  STAGE IVA                           9                           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 19(17Q12) MUTATED     8  22 111  16
  AMP PEAK 19(17Q12) WILD-TYPE  12  83 301  49
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                          8                           12
  T2                         22                           83
  T3                        111                          301
  T4                         16                           49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 19(17Q12) MUTATED    81  38  37
  AMP PEAK 19(17Q12) WILD-TYPE 260 110  75
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  N0                         81                          260
  N1                         38                          110
  N2                         37                           75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 19(17Q12) MUTATED   102  28   4   1  22
  AMP PEAK 19(17Q12) WILD-TYPE 344  46   6   1  41
D19V7, multiclass
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  M0                         102                          344
  M1                          28                           46
  M1A                          4                            6
  M1B                          1                            1
  MX                          22                           41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED    65  92
  AMP PEAK 19(17Q12) WILD-TYPE 218 229
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     65   92
  AMP PEAK 19(17Q12) WILD-TYPE  218  229
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  FEMALE                         65                          218
  MALE                           92                          229
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                     99
  AMP PEAK 19(17Q12) WILD-TYPE                  279
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                              11
  AMP PEAK 19(17Q12) WILD-TYPE                            48
                              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
D19V9, multiclass
                                clus
vv                               AMP PEAK 19(17Q12) MUTATED
  COLON ADENOCARCINOMA                                   99
  COLON MUCINOUS ADENOCARCINOMA                          11
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 19(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    279
  COLON MUCINOUS ADENOCARCINOMA                            48
  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"
D19V10, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED     1 156
  AMP PEAK 19(17Q12) WILD-TYPE   8 439
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      1  156
  AMP PEAK 19(17Q12) WILD-TYPE    8  439
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NO                           1                            8
  YES                        156                          439
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 19(17Q12) MUTATED   107   2  16   6
  AMP PEAK 19(17Q12) WILD-TYPE 329   3  20  23
D19V11, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  R0                        107                          329
  R1                          2                            3
  R2                         16                           20
  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                          18    71
  AMP PEAK 19(17Q12) WILD-TYPE                        38   221
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 19(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  38
  WHITE                                                     221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(17Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17Q24.1) MUTATED   120  15
  AMP PEAK 20(17Q24.1) WILD-TYPE 346  94
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           135                            440 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                            15                             94 
$`AMP PEAK 20(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2686 
        5.06         5.26        43.43        17.79        42.28        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       36.53        14.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 
       27.09        25.08        25.18        24.69        20.28         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 
       37.05         1.02        58.03        24.00        23.01        15.02 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 
       36.00        85.05        35.05         1.02        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3956 
       36.03         0.99        24.03        12.99        24.00        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
        2.01        21.99        50.99        13.05        34.06        27.02 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z 
       13.94        17.03        21.99        12.00         1.02        37.02 
TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         4.21         0.79         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-4948 
       16.31        61.41        29.56         2.24         0.07       102.44 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 
        8.02        13.02        29.06        22.03        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       29.03        21.99        14.99        13.05        11.08        11.01 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       12.26        19.59        11.51         1.32        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M 
       17.13        14.30        13.41       130.65         6.12        95.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       74.56        61.87        55.04        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A8F7 
       36.00        26.43        91.79        46.75         5.59         5.19 
TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-A56K 
       17.29        30.28        17.95        17.23        13.55        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       11.84        12.00         7.07        46.03        34.03        50.04 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 
       15.95        19.99        19.99        19.99        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A023 TCGA-AH-6643 
       17.03        15.95         9.07        31.00        51.98         0.69 
TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
        4.60         6.05        12.00        13.05        10.06       129.27 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       51.48         0.49         2.40        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6235 
        1.02         0.46        55.76 

$`AMP PEAK 20(17Q24.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        43.76        23.38        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        37.05        19.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04         0.99         0.99         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 
       15.95        38.99        36.95        37.02        14.93        33.07 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 
       26.01         2.01        20.98        16.08        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        19.07         7.96        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02        35.01        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.58         1.02         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        27.09         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82         5.19         5.52         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        65.00        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10         1.35        17.56        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-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-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        14.99        13.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       17.75        18.25         7.92        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         7.53        12.39        10.13        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-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       23.51        43.07        53.62        44.68        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        1.32         5.49        26.99         6.64        14.76        67.00 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       14.50         8.45        15.39        20.02        10.39        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        32.02         8.02         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
        1.02         2.01        12.03         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-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-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         1.02        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 
       38.04         0.49         1.45         0.72         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        36.00         7.10        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        41.36        57.24        24.13        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                         17.29                          17.90 
[1] "0.1 - 130.7 (17.3)" "0.1 - 140.4 (17.9)"
[1] "hr=" "2"  
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED   101  38
  AMP PEAK 20(17Q24.1) WILD-TYPE 337 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED    101   38
  AMP PEAK 20(17Q24.1) WILD-TYPE  337  124
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON                           101                            337
  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        41         2
  AMP PEAK 20(17Q24.1) WILD-TYPE      81        1       32       130         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(17Q24.1) MUTATED           1         5          4         20
  AMP PEAK 20(17Q24.1) WILD-TYPE         2        21         17         58
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(17Q24.1) MUTATED           12       18         8         1
  AMP PEAK 20(17Q24.1) WILD-TYPE         41       43        19         1
D20V4, multiclass
            clus
vv           AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  STAGE I                              21                             81
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            41                            130
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             5                             21
  STAGE IIIA                            4                             17
  STAGE IIIB                           20                             58
  STAGE IIIC                           12                             41
  STAGE IV                             18                             43
  STAGE IVA                             8                             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
  AMP PEAK 20(17Q24.1) MUTATED     4  24 100  12
  AMP PEAK 20(17Q24.1) WILD-TYPE  16  81 312  53
D20V5, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  T1                            4                             16
  T2                           24                             81
  T3                          100                            312
  T4                           12                             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 20(17Q24.1) MUTATED    78  35  26
  AMP PEAK 20(17Q24.1) WILD-TYPE 263 113  86
D20V6, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  N0                           78                            263
  N1                           35                            113
  N2                           26                             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 20(17Q24.1) MUTATED    94  21   4   1  20
  AMP PEAK 20(17Q24.1) WILD-TYPE 352  53   6   1  43
D20V7, multiclass
     clus
vv    AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  M0                            94                            352
  M1                            21                             53
  M1A                            4                              6
  M1B                            1                              1
  MX                            20                             43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED    69  71
  AMP PEAK 20(17Q24.1) WILD-TYPE 214 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED     69   71
  AMP PEAK 20(17Q24.1) WILD-TYPE  214  250
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  FEMALE                           69                            214
  MALE                             71                            250
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                     91
  AMP PEAK 20(17Q24.1) WILD-TYPE                  287
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                               9
  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
D20V9, multiclass
                                clus
vv                               AMP PEAK 20(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                     91
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      287
  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"
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED     1 139
  AMP PEAK 20(17Q24.1) WILD-TYPE   8 456
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED      1  139
  AMP PEAK 20(17Q24.1) WILD-TYPE    8  456
     clus
vv    AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  NO                             1                              8
  YES                          139                            456
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(17Q24.1) MUTATED   101   2  12   3
  AMP PEAK 20(17Q24.1) WILD-TYPE 335   3  24  26
D20V11, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  R0                          101                            335
  R1                            2                              3
  R2                           12                             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"
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                          15    71
  AMP PEAK 20(17Q24.1) WILD-TYPE                        41   221
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      71
                                  clus
vv                                 AMP PEAK 20(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.2) MUTATED    81  19
  AMP PEAK 21(19P13.2) WILD-TYPE 385  90
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           100                            475 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            19                             90 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 
        5.06         5.26        37.02        43.43        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       15.52        36.53        14.53        31.63        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 
       21.76        23.87        52.44         9.07         6.05         2.01 
TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 
       37.05        35.05         0.99        31.07        50.99        13.05 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O 
       27.02        13.94        42.02        32.02        51.98         0.92 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-A8YK 
        1.58         1.02         0.43         0.46        16.31         6.87 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       61.41        29.56        11.74         3.06         1.35        40.34 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
       21.99         2.01         8.02        13.02        29.06        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        14.04        29.03        21.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 
       13.02        11.08        19.59        13.51        15.12        11.38 
TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       49.91        35.97        74.56        45.11        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-A56K 
       26.43        47.15         5.19        17.23        10.39        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3896 
       65.98         1.02         6.05        19.99         0.99         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         0.99        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        10.98        11.01        12.00        36.00 
TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6512 
       13.05        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-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        23.38        17.79        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 
       13.94        37.05        37.25        16.04        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04         0.99         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07         7.96        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.20         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       61.87        53.62        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       17.29         6.64        14.76        30.28        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       14.50         8.45        15.39        20.02        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         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       32.02        19.99        14.04        17.03        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         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        15.02        12.99        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-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        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         86.63                         140.38 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         16.16                          17.98 
[1] "0.4 - 86.6 (16.2)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    73  36
  AMP PEAK 21(19P13.2) WILD-TYPE 365 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     73   36
  AMP PEAK 21(19P13.2) WILD-TYPE  365  126
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  COLON                            73                            365
  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        13        0        6        28         2
  AMP PEAK 21(19P13.2) WILD-TYPE      89        1       30       143         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(19P13.2) MUTATED           1         6          3         20
  AMP PEAK 21(19P13.2) WILD-TYPE         2        20         18         58
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(19P13.2) MUTATED           10       12         6         0
  AMP PEAK 21(19P13.2) WILD-TYPE         43       49        21         2
D21V4, multiclass
            clus
vv           AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            28                            143
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            3                             18
  STAGE IIIB                           20                             58
  STAGE IIIC                           10                             43
  STAGE IV                             12                             49
  STAGE IVA                             6                             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 21(19P13.2) MUTATED     2  14  80  13
  AMP PEAK 21(19P13.2) WILD-TYPE  18  91 332  52
D21V5, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  T1                            2                             18
  T2                           14                             91
  T3                           80                            332
  T4                           13                             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 21(19P13.2) MUTATED    54  36  19
  AMP PEAK 21(19P13.2) WILD-TYPE 287 112  93
D21V6, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  N0                           54                            287
  N1                           36                            112
  N2                           19                             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 21(19P13.2) MUTATED    74  15   3   0  16
  AMP PEAK 21(19P13.2) WILD-TYPE 372  59   7   2  47
D21V7, multiclass
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  M0                            74                            372
  M1                            15                             59
  M1A                            3                              7
  M1B                            0                              2
  MX                            16                             47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    45  64
  AMP PEAK 21(19P13.2) WILD-TYPE 238 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     45   64
  AMP PEAK 21(19P13.2) WILD-TYPE  238  257
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  FEMALE                           45                            238
  MALE                             64                            257
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                     66
  AMP PEAK 21(19P13.2) WILD-TYPE                  312
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                               7
  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
D21V9, multiclass
                                clus
vv                               AMP PEAK 21(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                     66
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 21(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      312
  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"
D21V10, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED     1 108
  AMP PEAK 21(19P13.2) WILD-TYPE   8 487
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED      1  108
  AMP PEAK 21(19P13.2) WILD-TYPE    8  487
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  NO                             1                              8
  YES                          108                            487
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(19P13.2) MUTATED    79   3   6   7
  AMP PEAK 21(19P13.2) WILD-TYPE 357   2  30  22
D21V11, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  R0                           79                            357
  R1                            3                              2
  R2                            6                             30
  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                          15    57
  AMP PEAK 21(19P13.2) WILD-TYPE                        41   235
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 21(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(19Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(19Q12) MUTATED   104  21
  AMP PEAK 22(19Q12) WILD-TYPE 362  88
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         125                          450 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          21                           88 
$`AMP PEAK 22(19Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
        5.06         5.26        37.02        43.43        45.60        15.52 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 
       16.04        34.65        36.53        14.53        31.63        29.16 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       25.08        25.18        21.76        23.87        61.84        52.44 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 TCGA-AA-3812 
       35.01        58.03        12.99        13.02        37.05        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 TCGA-AA-3972 
        0.99        37.02        33.07        36.03        12.99        50.99 
TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01G 
       13.05        18.05        27.02        42.02        21.99        12.00 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 TCGA-AD-6899 
       51.98         2.96        39.98         0.92         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D 
        1.02         0.20         0.43        14.50         0.20         5.52 
TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 
        6.87        61.41        29.56        11.74         3.06         1.35 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 
       40.34        21.99         2.01        37.02         8.02        13.02 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       16.01         5.03        15.02        15.02        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 
       21.99        11.08        19.59        15.12         4.50        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 
       13.41        12.00        11.38       119.70        35.97         8.61 
TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       35.41        82.39        74.56        45.11        39.42        26.43 
TCGA-G4-6627 TCGA-NH-A8F7 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-A56K TCGA-AF-A56L 
       47.15         5.19        17.95        10.39        86.63        65.98 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 
        1.02        46.03         6.05        19.99         0.99        19.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        1.02        36.03         1.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-BM-6198 TCGA-CI-6619 
       12.00        31.00         1.94        38.04        10.19         6.05 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 
        4.73        13.97        10.98        11.01        12.00        36.00 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6512 
       13.05       129.27        24.13         0.49        20.55        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 
       16.31        11.51        13.64        11.97         0.76 

$`AMP PEAK 22(19Q12) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        23.38        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       35.11        13.94        37.05        37.25        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       32.71        27.09        22.52        24.13         8.38        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05         1.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03         0.99        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       16.08        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.10         0.76         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.95        15.75        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        65.00        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01         5.23         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       30.08        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         1.32         7.92        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         9.04         9.44         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
      119.93        60.79       117.07        98.24        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 
       19.43       107.67        28.21         8.35        23.51        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       61.87        53.62        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        91.79        46.75        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.52         2.79         5.98         5.59         1.32         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
       29.98         1.02        32.98         0.99         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-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        14.04        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
        4.60         1.81         6.05         6.97         9.37        60.03 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        15.02        12.99        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       57.24        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-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.46        18.28        55.76        47.08        26.43 

  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                        0.20                         0.07 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                      129.27                       140.38 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                       15.95                        18.05 
[1] "0.2 - 129.3 (15.9)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    92  44
  AMP PEAK 22(19Q12) WILD-TYPE 346 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     92   44
  AMP PEAK 22(19Q12) WILD-TYPE  346  118
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  COLON                          92                          346
  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        21        0        5        35         1
  AMP PEAK 22(19Q12) WILD-TYPE      81        1       31       136         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(19Q12) MUTATED           1         5          4         21
  AMP PEAK 22(19Q12) WILD-TYPE         2        21         17         57
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(19Q12) MUTATED           12       22         6         0
  AMP PEAK 22(19Q12) WILD-TYPE         41       39        21         2
D22V4, multiclass
            clus
vv           AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  STAGE I                            21                           81
  STAGE IA                            0                            1
  STAGE II                            5                           31
  STAGE IIA                          35                          136
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          4                           17
  STAGE IIIB                         21                           57
  STAGE IIIC                         12                           41
  STAGE IV                           22                           39
  STAGE IVA                           6                           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 22(19Q12) MUTATED     3  22  95  16
  AMP PEAK 22(19Q12) WILD-TYPE  17  83 317  49
D22V5, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  T1                          3                           17
  T2                         22                           83
  T3                         95                          317
  T4                         16                           49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 22(19Q12) MUTATED    67  42  26
  AMP PEAK 22(19Q12) WILD-TYPE 274 106  86
D22V6, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  N0                         67                          274
  N1                         42                          106
  N2                         26                           86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 22(19Q12) MUTATED    89  24   4   0  17
  AMP PEAK 22(19Q12) WILD-TYPE 357  50   6   2  46
D22V7, multiclass
     clus
vv    AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  M0                          89                          357
  M1                          24                           50
  M1A                          4                            6
  M1B                          0                            2
  MX                          17                           46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    57  79
  AMP PEAK 22(19Q12) WILD-TYPE 226 242
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     57   79
  AMP PEAK 22(19Q12) WILD-TYPE  226  242
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  FEMALE                         57                          226
  MALE                           79                          242
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                     83
  AMP PEAK 22(19Q12) WILD-TYPE                  295
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                               9
  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
D22V9, multiclass
                                clus
vv                               AMP PEAK 22(19Q12) MUTATED
  COLON ADENOCARCINOMA                                   83
  COLON MUCINOUS ADENOCARCINOMA                           9
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          0
                                clus
vv                               AMP PEAK 22(19Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    295
  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"
D22V10, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED     2 134
  AMP PEAK 22(19Q12) WILD-TYPE   7 461
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED      2  134
  AMP PEAK 22(19Q12) WILD-TYPE    7  461
     clus
vv    AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  NO                           2                            7
  YES                        134                          461
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(19Q12) MUTATED    96   2  11   7
  AMP PEAK 22(19Q12) WILD-TYPE 340   3  25  22
D22V11, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  R0                         96                          340
  R1                          2                            3
  R2                         11                           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"
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                          16    70
  AMP PEAK 22(19Q12) WILD-TYPE                        40   222
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                16
  WHITE                                                    70
                                  clus
vv                                 AMP PEAK 22(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                  40
  WHITE                                                     222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(20P12.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(20P12.1) MUTATED   209  50
  AMP PEAK 23(20P12.1) WILD-TYPE 257  59
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           259                            316 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                            50                             59 
$`AMP PEAK 23(20P12.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       45.60        13.94        15.52        16.04        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6649 
       32.45        32.91        30.44        27.09        25.08        24.16 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.69        20.28        61.84         9.63         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3530 
        1.02        58.03         6.97         1.02        24.03        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 
       29.00        29.00        14.01        21.01        13.02        23.01 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        19.99         6.05         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.05        15.02        37.05        19.00        36.00         5.03 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99         0.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3939 
       33.07         0.99        31.07        17.03        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       24.00        34.03        21.99        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       26.01        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       18.05        17.03         4.01        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X 
       15.02         0.99        12.00        31.00        33.04        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
       51.98         2.96         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       39.98         0.07         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D 
        0.10         0.43        16.31         0.95         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-6598 
        6.87         1.41         5.13        83.80        65.00        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 
        3.29         0.07         1.35        17.56        40.34        48.20 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 
       20.02         8.02        13.02        29.06        22.98         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       21.99        14.04        11.01        11.08        11.01        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6920 
       12.26        19.59        20.19        17.75        12.49        12.39 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 
       10.13         9.04        11.64        13.41        10.26       119.70 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       12.59         7.50        44.32       139.17         6.12        14.04 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 
       35.97       117.07        95.18         8.61        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 
        1.55        35.41       107.67        28.21        82.39        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        35.93        36.00        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC 
       91.79        46.75        47.15         4.11         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 
        5.19        26.99        17.29        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         8.45        20.02        10.39 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 
        8.02         1.02         1.02        46.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3878 
        0.99        19.99        19.99        29.98         1.02         0.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4005 
       36.95        17.03        14.01        48.03        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        17.03         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       36.03         9.07        51.98        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.97         9.37        13.97        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A0XA 
       12.99        13.97        15.02        36.00        12.95       126.44 
TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 
      129.27        20.55        20.91        17.00        18.28        16.31 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       13.64        11.97         9.96        37.51         0.39         1.02 
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 
TCGA-G5-6572 
       47.08 

$`AMP PEAK 23(20P12.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2684 
        5.26        46.65        23.38        17.79        42.28        37.05 
TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       37.25        14.53        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        52.44         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 
       37.05         1.02        35.01        63.98        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-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 
       34.03        26.01        12.99         0.99        33.99        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        6.97        54.02         0.92        47.01        11.01         5.98 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3819 
       85.05        26.99        19.04         0.99        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3854 
        1.02        17.98        15.95        38.99        36.95        36.03 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       32.05        31.07        53.00        24.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       20.98         2.01        16.08        25.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
        0.99        34.98        15.02        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       39.98        22.03        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       56.55         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 
       27.09        15.75         0.20        21.44        17.82        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
       50.37        58.39         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       61.41         6.77       100.01         5.23        11.74         1.94 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 
        3.25         0.26         0.33         0.10       102.44        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        37.02        26.04         8.02        27.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 
       22.03        30.08        16.01        15.02        12.00        29.03 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       11.08        10.06        12.03        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58         7.53        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
        9.44         1.51        12.00        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      135.65         7.76        26.47        81.37       119.93        60.79 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 
       98.24        13.38        11.11        13.64        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67         1.28         0.53        19.43 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 
       44.68        51.75        36.72        26.43        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        52.80        10.98        10.52         2.79         5.98 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 
        5.49         6.64        14.76        30.28        67.00        17.95 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       43.04        13.55        12.72        15.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 
       24.00        34.03         2.01         6.05        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 
        0.99        32.98         0.99        19.99         1.02        13.02 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4022 
       35.01         1.02        32.02        28.04        36.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       20.98        13.94        15.95         1.02        12.00        31.00 
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-AH-6547 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       61.97         1.45         6.05         4.73        60.03         7.99 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       12.00         7.10        30.05        13.05        10.06         5.29 
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-6507 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
        2.40        19.96        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
        8.61        11.51        10.78        17.46         8.45        31.30 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
       14.86         0.69         0.46        26.43 

  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                        139.17                         140.38 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                         15.52                          20.27 
[1] "0.1 - 139.2 (15.5)" "0.1 - 140.4 (20.3)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   190  81
  AMP PEAK 23(20P12.1) WILD-TYPE 248  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    190   81
  AMP PEAK 23(20P12.1) WILD-TYPE  248   81
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  COLON                           190                            248
  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        49        1       10        68         4
  AMP PEAK 23(20P12.1) WILD-TYPE      53        0       26       103         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20P12.1) MUTATED           1        10         13         29
  AMP PEAK 23(20P12.1) WILD-TYPE         2        16          8         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20P12.1) MUTATED           23       42        14         1
  AMP PEAK 23(20P12.1) WILD-TYPE         30       19        13         1
D23V4, multiclass
            clus
vv           AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  STAGE I                              49                             53
  STAGE IA                              1                              0
  STAGE II                             10                             26
  STAGE IIA                            68                            103
  STAGE IIB                             4                              6
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                           13                              8
  STAGE IIIB                           29                             49
  STAGE IIIC                           23                             30
  STAGE IV                             42                             19
  STAGE IVA                            14                             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  51 183  29
  AMP PEAK 23(20P12.1) WILD-TYPE  11  54 229  36
D23V5, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  T1                            9                             11
  T2                           51                             54
  T3                          183                            229
  T4                           29                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 23(20P12.1) MUTATED   142  74  56
  AMP PEAK 23(20P12.1) WILD-TYPE 199  74  56
D23V6, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  N0                          142                            199
  N1                           74                             74
  N2                           56                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 23(20P12.1) MUTATED   183  45   8   1  32
  AMP PEAK 23(20P12.1) WILD-TYPE 263  29   2   1  31
D23V7, multiclass
     clus
vv    AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  M0                           183                            263
  M1                            45                             29
  M1A                            8                              2
  M1B                            1                              1
  MX                            32                             31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   115 159
  AMP PEAK 23(20P12.1) WILD-TYPE 168 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    115  159
  AMP PEAK 23(20P12.1) WILD-TYPE  168  162
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  FEMALE                          115                            168
  MALE                            159                            162
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                    172
  AMP PEAK 23(20P12.1) WILD-TYPE                  206
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                              17
  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
D23V9, multiclass
                                clus
vv                               AMP PEAK 23(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    172
  COLON MUCINOUS ADENOCARCINOMA                            17
  RECTAL ADENOCARCINOMA                                    76
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK 23(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      206
  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"
D23V10, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED     7 267
  AMP PEAK 23(20P12.1) WILD-TYPE   2 328
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED      7  267
  AMP PEAK 23(20P12.1) WILD-TYPE    2  328
     clus
vv    AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  NO                             7                              2
  YES                          267                            328
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(20P12.1) MUTATED   194   3  23  10
  AMP PEAK 23(20P12.1) WILD-TYPE 242   2  13  19
D23V11, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  R0                          194                            242
  R1                            3                              2
  R2                           23                             13
  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                          23   132
  AMP PEAK 23(20P12.1) WILD-TYPE                        33   160
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK 23(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    33
  WHITE                                                       160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(20P11.21) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(20P11.21) MUTATED   274  64
  AMP PEAK 24(20P11.21) WILD-TYPE 192  45
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            338                             237 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                             64                              45 
$`AMP PEAK 24(20P11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        15.52        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       24.16        24.69        20.28        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 
        1.02         1.02         1.02        58.03         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       38.99        19.07        29.00        29.00        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       21.01        13.02        23.01        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        0.99        25.02        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        0.99        33.07         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K 
       24.00        27.02        19.07         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       17.03         4.01        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X 
       15.02         0.99        12.00        31.00        33.04        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
       41.00        39.98        40.96         0.07        21.37         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         1.58         1.02         0.10         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D 
       14.50        16.31         0.95         0.20         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        6.87         1.41         5.13        83.80        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       49.41        12.10        29.56         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56        40.34        48.20        21.99        20.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        13.02        29.06        22.03        22.98        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       29.03        16.04        21.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        11.08        11.01        10.06        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        11.51        20.19        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
        7.92        12.49         7.53        12.39        10.13         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       11.64        13.41        10.26       119.70        24.43       130.65 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       12.59         7.50       131.51       139.17         6.12        14.04 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       13.45         6.18         1.55        33.67         1.28        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
      107.67        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15         4.11 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         1.32         5.19        26.99        17.29         6.64 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
        8.45        20.02        10.39        86.63        11.84        36.03 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        8.02         7.07         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
       12.03        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       64.01        51.98        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG 
       12.95        13.05       126.44        41.36       129.27        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        0.49        20.55        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.31        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 24(20P11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 
        5.26        46.65        23.38        42.28        37.05        37.25 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 
       19.66        16.24        24.92        52.44         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       35.01        63.98        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3538 
       37.05        36.03         8.05        19.07        34.03        26.01 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 
        0.99        33.99        24.00        17.95        29.95        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       13.94        61.02         6.97        54.02         0.92        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       11.01         5.98        26.99        19.04         0.99        35.05 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3855 
        1.02        17.98        15.95        36.95        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        24.03        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
       42.02         0.99        34.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 
       22.03        18.05         4.21        56.55         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 
        0.92        27.09        15.75        21.44        17.82        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
       50.37        58.39         5.65        32.94        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01         5.23        11.74         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.10       102.44        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       27.02        30.08        15.02        12.00        14.99        12.99 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 
       12.95        13.05        11.08        12.03        13.51        20.42 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        17.13        16.14        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.44         1.51        12.00        11.38 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      135.65         7.76        26.47        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.64        35.87        16.31        29.59        16.24 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
        0.53        19.43        74.56        43.07        53.62        51.75 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       36.00        26.43        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z2 
       10.98        10.52         2.79         5.98         5.49        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 
       30.28        67.00        43.04        13.55        12.72        14.50 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3584 
       15.39        65.98        12.00        32.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3732 
        1.02         2.01         6.05         0.99         0.99        32.98 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       13.02        35.01        28.04         0.99        20.98        13.94 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        1.02        31.00        70.03        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-6158 
       38.96        61.97         1.45         6.05         4.73         7.10 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       30.05        10.06         5.29        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        2.40        19.96        15.85        16.34        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
       17.46         8.45        31.30 

  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                          16.04                           21.44 
[1] "0.1 - 139.2 (16.0)" "0.1 - 140.4 (21.4)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   243 110
  AMP PEAK 24(20P11.21) WILD-TYPE 195  52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    243  110
  AMP PEAK 24(20P11.21) WILD-TYPE  195   52
        clus
vv       AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  COLON                            243                             195
  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        62        1       16        95         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         17         40
  AMP PEAK 24(20P11.21) WILD-TYPE         1        15          4         38
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20P11.21) MUTATED           30       47        18         1
  AMP PEAK 24(20P11.21) WILD-TYPE         23       14         9         1
D24V4, multiclass
            clus
vv           AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  STAGE I                               62                              40
  STAGE IA                               1                               0
  STAGE II                              16                              20
  STAGE IIA                             95                              76
  STAGE IIB                              5                               5
  STAGE IIC                              2                               1
  STAGE III                             11                              15
  STAGE IIIA                            17                               4
  STAGE IIIB                            40                              38
  STAGE IIIC                            30                              23
  STAGE IV                              47                              14
  STAGE IVA                             18                               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  65 239  36
  AMP PEAK 24(20P11.21) WILD-TYPE   7  40 173  29
D24V5, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  T1                            13                               7
  T2                            65                              40
  T3                           239                             173
  T4                            36                              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 24(20P11.21) MUTATED   193  94  66
  AMP PEAK 24(20P11.21) WILD-TYPE 148  54  46
D24V6, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  N0                           193                             148
  N1                            94                              54
  N2                            66                              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 24(20P11.21) MUTATED   246  54   9   1  39
  AMP PEAK 24(20P11.21) WILD-TYPE 200  20   1   1  24
D24V7, multiclass
     clus
vv    AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  M0                            246                             200
  M1                             54                              20
  M1A                             9                               1
  M1B                             1                               1
  MX                             39                              24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   155 200
  AMP PEAK 24(20P11.21) WILD-TYPE 128 121
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    155  200
  AMP PEAK 24(20P11.21) WILD-TYPE  128  121
        clus
vv       AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  FEMALE                           155                             128
  MALE                             200                             121
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                    221
  AMP PEAK 24(20P11.21) WILD-TYPE                  157
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                              21
  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
D24V9, multiclass
                                clus
vv                               AMP PEAK 24(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                     221
  COLON MUCINOUS ADENOCARCINOMA                             21
  RECTAL ADENOCARCINOMA                                    105
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               AMP PEAK 24(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       157
  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"
D24V10, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED     7 348
  AMP PEAK 24(20P11.21) WILD-TYPE   2 247
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED      7  348
  AMP PEAK 24(20P11.21) WILD-TYPE    2  247
     clus
vv    AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  NO                              7                               2
  YES                           348                             247
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 24(20P11.21) MUTATED   254   3  25  14
  AMP PEAK 24(20P11.21) WILD-TYPE 182   2  11  15
D24V11, multiclass
    clus
vv   AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  R0                           254                             182
  R1                             3                               2
  R2                            25                              11
  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                          29   179
  AMP PEAK 24(20P11.21) WILD-TYPE                        27   113
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      179
                                  clus
vv                                 AMP PEAK 24(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        113
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(20Q11.21) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(20Q11.21) MUTATED   356  82
  AMP PEAK 25(20Q11.21) WILD-TYPE 110  27
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            438                             137 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                             82                              27 
$`AMP PEAK 25(20Q11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
        0.99        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        15.75         0.20         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         1.41         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        49.41        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       21.99         2.01        20.02        37.02         8.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        17.13        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       35.97       117.07        95.18         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       39.42        35.93        36.72        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       13.78        91.79        46.75        47.15         4.11        10.52 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        6.64        30.28        24.13        17.95        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-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-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        51.98         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-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 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06       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-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 25(20Q11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        61.02         6.97        54.02         0.92 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
       11.01        26.99        19.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       15.95        36.03        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F 
        1.02        35.01        35.01        39.06        22.03        18.05 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       56.55         0.76         0.92        27.09        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       50.37        58.39         5.65        32.94        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
      100.01        11.74         3.25         0.33         0.10        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 
       26.04        27.02        15.02        12.00        12.95        13.05 
TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 
       12.03        20.42        16.14        15.58         9.44         1.51 
TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G 
       12.00       140.38       135.65         7.76        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 
       98.24        11.11        35.87        16.31        19.43        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       43.07        53.62        51.75        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       52.80        10.98         2.79         5.98        14.76        67.00 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        12.72        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CI-6620 
       32.98        13.02        20.98        49.97        61.97         6.05 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        5.29        19.96         8.61        17.46         8.45 

  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                          17.03                           21.14 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.1)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   312 144
  AMP PEAK 25(20Q11.21) WILD-TYPE 126  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    312  144
  AMP PEAK 25(20Q11.21) WILD-TYPE  126   18
        clus
vv       AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  COLON                            312                             126
  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        77        1       21       117         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        19         20         62
  AMP PEAK 25(20Q11.21) WILD-TYPE         0         7          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(20Q11.21) MUTATED           44       55        23         1
  AMP PEAK 25(20Q11.21) WILD-TYPE          9        6         4         1
D25V4, multiclass
            clus
vv           AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  STAGE I                               77                              25
  STAGE IA                               1                               0
  STAGE II                              21                              15
  STAGE IIA                            117                              54
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             19                               7
  STAGE IIIA                            20                               1
  STAGE IIIB                            62                              16
  STAGE IIIC                            44                               9
  STAGE IV                              55                               6
  STAGE IVA                             23                               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  84 315  44
  AMP PEAK 25(20Q11.21) WILD-TYPE   6  21  97  21
D25V5, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  T1                            14                               6
  T2                            84                              21
  T3                           315                              97
  T4                            44                              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 25(20Q11.21) MUTATED   239 126  91
  AMP PEAK 25(20Q11.21) WILD-TYPE 102  22  21
D25V6, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  N0                           239                             102
  N1                           126                              22
  N2                            91                              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 25(20Q11.21) MUTATED   329  66   9   1  48
  AMP PEAK 25(20Q11.21) WILD-TYPE 117   8   1   1  15
D25V7, multiclass
     clus
vv    AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  M0                            329                             117
  M1                             66                               8
  M1A                             9                               1
  M1B                             1                               1
  MX                             48                              15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   209 250
  AMP PEAK 25(20Q11.21) WILD-TYPE  74  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    209  250
  AMP PEAK 25(20Q11.21) WILD-TYPE   74   71
        clus
vv       AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  FEMALE                           209                              74
  MALE                             250                              71
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                    286
  AMP PEAK 25(20Q11.21) WILD-TYPE                   92
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                              25
  AMP PEAK 25(20Q11.21) WILD-TYPE                            34
                                 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
D25V9, multiclass
                                clus
vv                               AMP PEAK 25(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                     286
  COLON MUCINOUS ADENOCARCINOMA                             25
  RECTAL ADENOCARCINOMA                                    135
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 25(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                        92
  COLON MUCINOUS ADENOCARCINOMA                               34
  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"
D25V10, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED     8 451
  AMP PEAK 25(20Q11.21) WILD-TYPE   1 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED      8  451
  AMP PEAK 25(20Q11.21) WILD-TYPE    1  144
     clus
vv    AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  NO                              8                               1
  YES                           451                             144
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 25(20Q11.21) MUTATED   329   4  32  17
  AMP PEAK 25(20Q11.21) WILD-TYPE 107   1   4  12
D25V11, multiclass
    clus
vv   AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  R0                           329                             107
  R1                             4                               1
  R2                            32                               4
  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                          40   228
  AMP PEAK 25(20Q11.21) WILD-TYPE                        16    64
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      228
                                  clus
vv                                 AMP PEAK 25(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                         64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(20Q12) MUTATION ANALYSIS
D26V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 26(20Q12) MUTATED   358  82
  AMP PEAK 26(20Q12) WILD-TYPE 108  27
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         440                          135 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                          82                           27 
$`AMP PEAK 26(20Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       35.05         0.99        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        19.07         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        17.03         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         0.46        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
        0.20         5.19         5.52         6.87        75.25         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        2.01        20.02        37.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.50        17.13        12.49         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.43        14.30         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       82.39        23.51        74.56        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15         4.11 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.52         5.59         1.32         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        30.28        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 26(20Q12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        61.02         6.97        54.02         0.92 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 
       11.01         5.98        26.99        19.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 
       17.98        15.95        36.03        53.00        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
        0.99        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       22.03        18.05        56.55         0.76         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 
       21.44        17.82        50.37        58.39        32.94        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
        6.77       100.01        11.74         3.25         0.33         0.10 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 
       23.05        26.04        27.02        15.02        12.00        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 
       13.05        12.03        20.42        16.14        15.58         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
        1.51        12.00       140.38       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        35.87        19.43        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       53.62        51.75        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 
       10.98         2.79         5.98        14.76        67.00        13.55 
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       12.72        12.00        32.02         2.01         6.05        32.98 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 
       13.02        20.98        49.97        61.97         5.29        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        8.61        17.46         8.45 

  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                        0.07                         0.10 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                      139.17                       140.38 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                       17.03                        21.14 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.1)"
[1] "hr=" "1.1"
D26V2, continuous
D26V3, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   313 145
  AMP PEAK 26(20Q12) WILD-TYPE 125  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    313  145
  AMP PEAK 26(20Q12) WILD-TYPE  125   17
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  COLON                         313                          125
  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        77        1       21       118         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        18         20         62
  AMP PEAK 26(20Q12) WILD-TYPE         0         8          1         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 26(20Q12) MUTATED           44       55        25         1
  AMP PEAK 26(20Q12) WILD-TYPE          9        6         2         1
D26V4, multiclass
            clus
vv           AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  STAGE I                            77                           25
  STAGE IA                            1                            0
  STAGE II                           21                           15
  STAGE IIA                         118                           53
  STAGE IIB                           5                            5
  STAGE IIC                           3                            0
  STAGE III                          18                            8
  STAGE IIIA                         20                            1
  STAGE IIIB                         62                           16
  STAGE IIIC                         44                            9
  STAGE IV                           55                            6
  STAGE IVA                          25                            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  84 316  45
  AMP PEAK 26(20Q12) WILD-TYPE   6  21  96  20
D26V5, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  T1                         14                            6
  T2                         84                           21
  T3                        316                           96
  T4                         45                           20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 26(20Q12) MUTATED   240 127  91
  AMP PEAK 26(20Q12) WILD-TYPE 101  21  21
D26V6, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  N0                        240                          101
  N1                        127                           21
  N2                         91                           21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 26(20Q12) MUTATED   329  68   9   1  48
  AMP PEAK 26(20Q12) WILD-TYPE 117   6   1   1  15
D26V7, multiclass
     clus
vv    AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  M0                         329                          117
  M1                          68                            6
  M1A                          9                            1
  M1B                          1                            1
  MX                          48                           15
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   210 251
  AMP PEAK 26(20Q12) WILD-TYPE  73  70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    210  251
  AMP PEAK 26(20Q12) WILD-TYPE   73   70
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  FEMALE                        210                           73
  MALE                          251                           70
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                    288
  AMP PEAK 26(20Q12) WILD-TYPE                   90
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                              24
  AMP PEAK 26(20Q12) WILD-TYPE                            35
                              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
D26V9, multiclass
                                clus
vv                               AMP PEAK 26(20Q12) MUTATED
  COLON ADENOCARCINOMA                                  288
  COLON MUCINOUS ADENOCARCINOMA                          24
  RECTAL ADENOCARCINOMA                                 136
  RECTAL MUCINOUS ADENOCARCINOMA                          7
                                clus
vv                               AMP PEAK 26(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                     90
  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"
D26V10, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED     8 453
  AMP PEAK 26(20Q12) WILD-TYPE   1 142
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED      8  453
  AMP PEAK 26(20Q12) WILD-TYPE    1  142
     clus
vv    AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  NO                           8                            1
  YES                        453                          142
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(20Q12) MUTATED   330   4  32  17
  AMP PEAK 26(20Q12) WILD-TYPE 106   1   4  12
D26V11, multiclass
    clus
vv   AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  R0                        330                          106
  R1                          4                            1
  R2                         32                            4
  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                          40   232
  AMP PEAK 26(20Q12) WILD-TYPE                        16    60
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                40
  WHITE                                                   232
                                  clus
vv                                 AMP PEAK 26(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(20Q13.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q13.31) MUTATED   360  83
  AMP PEAK 27(20Q13.31) WILD-TYPE 106  26
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            443                             132 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                             83                              26 
$`AMP PEAK 27(20Q13.31) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 
       85.05         0.99        35.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05        12.99        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       26.01        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
        0.99        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        15.75         0.20         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         1.41         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       48.20        21.99         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.50        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       131.51       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       47.15         4.11        10.52         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 
        5.49        26.99        17.29         6.64        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       86.63        65.98        11.84        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 27(20Q13.31) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3680 
       17.95        29.95        61.02         6.97         0.92        11.01 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        19.04         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        53.00        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        24.00         2.01        25.02        27.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q 
       30.02        18.05         0.99        34.98        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
       35.01        35.01        39.06        22.03        18.05        56.55 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
        0.76         0.20         0.92        27.09        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       50.37        58.39         5.65        32.94        61.41         6.77 
TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
      100.01         3.25         0.33         0.10        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       51.32        21.14         2.93       124.27        23.05        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       27.02        15.02        12.00        12.95        13.05        12.03 
TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       20.42        16.14        15.58         9.44         1.51        12.00 
TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      140.38       135.65         7.76        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       11.11        35.87        19.43        43.07        53.62        51.75 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       22.09        35.80        26.17        52.80        10.98         2.79 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
        5.98        14.76        67.00        12.72        12.00        32.02 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 
        2.01         6.05        32.98        13.02        20.98        49.97 
TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       61.97         5.29        19.96         8.61        17.46         8.45 

  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                          17.03                           21.29 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.3)"
[1] "hr=" "1.1"
D27V2, continuous
D27V3, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   315 145
  AMP PEAK 27(20Q13.31) WILD-TYPE 123  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    315  145
  AMP PEAK 27(20Q13.31) WILD-TYPE  123   17
        clus
vv       AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  COLON                            315                             123
  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        77        1       22       119         5
  AMP PEAK 27(20Q13.31) WILD-TYPE      25        0       14        52         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(20Q13.31) MUTATED           3        19         20         62
  AMP PEAK 27(20Q13.31) WILD-TYPE         0         7          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 27(20Q13.31) MUTATED           45       56        24         1
  AMP PEAK 27(20Q13.31) WILD-TYPE          8        5         3         1
D27V4, multiclass
            clus
vv           AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  STAGE I                               77                              25
  STAGE IA                               1                               0
  STAGE II                              22                              14
  STAGE IIA                            119                              52
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             19                               7
  STAGE IIIA                            20                               1
  STAGE IIIB                            62                              16
  STAGE IIIC                            45                               8
  STAGE IV                              56                               5
  STAGE IVA                             24                               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  84 320  44
  AMP PEAK 27(20Q13.31) WILD-TYPE   6  21  92  21
D27V5, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  T1                            14                               6
  T2                            84                              21
  T3                           320                              92
  T4                            44                              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 27(20Q13.31) MUTATED   242 127  92
  AMP PEAK 27(20Q13.31) WILD-TYPE  99  21  20
D27V6, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  N0                           242                              99
  N1                           127                              21
  N2                            92                              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 27(20Q13.31) MUTATED   333  68   9   1  47
  AMP PEAK 27(20Q13.31) WILD-TYPE 113   6   1   1  16
D27V7, multiclass
     clus
vv    AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  M0                            333                             113
  M1                             68                               6
  M1A                             9                               1
  M1B                             1                               1
  MX                             47                              16
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   213 251
  AMP PEAK 27(20Q13.31) WILD-TYPE  70  70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    213  251
  AMP PEAK 27(20Q13.31) WILD-TYPE   70   70
        clus
vv       AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  FEMALE                           213                              70
  MALE                             251                              70
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                    289
  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                            34
                                 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
D27V9, multiclass
                                clus
vv                               AMP PEAK 27(20Q13.31) MUTATED
  COLON ADENOCARCINOMA                                     289
  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                               34
  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"
D27V10, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED     8 456
  AMP PEAK 27(20Q13.31) WILD-TYPE   1 139
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED      8  456
  AMP PEAK 27(20Q13.31) WILD-TYPE    1  139
     clus
vv    AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  NO                              8                               1
  YES                           456                             139
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 27(20Q13.31) MUTATED   333   4  32  17
  AMP PEAK 27(20Q13.31) WILD-TYPE 103   1   4  12
D27V11, multiclass
    clus
vv   AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  R0                           333                             103
  R1                             4                               1
  R2                            32                               4
  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                          40   232
  AMP PEAK 27(20Q13.31) WILD-TYPE                        16    60
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      232
                                  clus
vv                                 AMP PEAK 27(20Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                         60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   179  50
  DEL PEAK  1(1P36.11) WILD-TYPE 287  59
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           229                            346 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            50                             59 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        17.79        44.91        35.11        13.94        15.52 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       36.53        14.53        32.45        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       29.16        22.52        24.13        25.18        21.76        23.87 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 
       52.44         5.03        38.99         9.07        37.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       19.07        34.03        14.01        13.02        24.00        23.01 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       19.99         2.01        14.01        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 
       19.00        36.00        85.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 
       31.07        31.07        17.03        24.03        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       12.99         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       26.01         7.96        34.03        42.02        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03        41.00        40.96         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
        5.52         5.65         5.13        22.36        65.00        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
        3.29         0.07         0.26         1.35        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02         8.02        13.02        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       15.02        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        10.06        12.03        14.99        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6541 
       17.75         1.32         7.92        15.12        17.85        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.43        14.30        13.41        11.38        92.75        49.91 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28M 
       44.32       139.17         6.12        26.47       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 
       13.38        11.11         1.55        29.59         1.28        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 
        8.35        82.39        23.51        61.87        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       36.00        91.79        46.75         4.11        10.98         5.98 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        5.49        26.99        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       19.10        10.39        14.50        15.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       11.84        32.02         1.02         2.01        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       34.03         6.05        19.99         0.99        29.98         1.02 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
       19.99         1.02        36.95        17.03         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       19.99        28.04        36.03        13.94        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        51.98         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 
       38.04         0.49         0.69         0.72        10.19         6.97 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
        4.73        11.01        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE 
       36.00        30.05        12.95        10.06       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 
       32.61         0.49         2.40        20.55        15.85        11.97 
TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
        8.45        14.86         1.02         0.69         0.46        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        45.60        37.05        37.25        16.04        34.65 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       27.09         8.38        25.08        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3532 
       13.02         1.02        24.03        36.03         8.05        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.05         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        17.03        36.03        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       34.03        16.08        34.06        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        34.98         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.10         0.76         0.92        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        21.44        17.82         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5403 
       50.37        58.39         1.41        32.94        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       61.41        49.41         6.77       100.01        11.74         1.94 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        48.20        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.98        16.01        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 
       14.04        12.95        13.05        11.08        11.01        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       19.59        11.51        20.42        18.25         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
       12.49        16.14         7.53        12.39        10.13         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C 
        7.50       131.51       135.65         7.76        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 
      119.93        35.97        60.79        98.24         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18        35.87        16.31        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43       107.67        28.21        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       47.15        52.80        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        5.19        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       17.95        12.72        37.74         8.45        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 
       36.03        12.00         8.02         7.07         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       32.98         0.99         0.99        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       32.02        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-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-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       31.00        10.98        49.97        61.97        41.00         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-4957 
        4.60         1.81         6.05         6.05         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 
       60.03         7.99        10.98        15.02         7.10        13.05 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6507 
        5.29        41.36        57.24        24.13        51.48        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 
        9.96        37.51        31.30         0.39         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        1.12         0.76        18.28        55.76 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         17.03                          18.05 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   163  73
  DEL PEAK  1(1P36.11) WILD-TYPE 275  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    163   73
  DEL PEAK  1(1P36.11) WILD-TYPE  275   89
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  COLON                           163                            275
  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        62         3
  DEL PEAK  1(1P36.11) WILD-TYPE      69        1       28       109         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1        10          7         29
  DEL PEAK  1(1P36.11) WILD-TYPE         2        16         14         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           26       37        16         0
  DEL PEAK  1(1P36.11) WILD-TYPE         27       24        11         2
D28V4, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              33                             69
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            62                            109
  STAGE IIB                             3                              7
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            7                             14
  STAGE IIIB                           29                             49
  STAGE IIIC                           26                             27
  STAGE IV                             37                             24
  STAGE IVA                            16                             11
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED     5  40 162  31
  DEL PEAK  1(1P36.11) WILD-TYPE  15  65 250  34
D28V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            5                             15
  T2                           40                             65
  T3                          162                            250
  T4                           31                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  1(1P36.11) MUTATED   116  64  57
  DEL PEAK  1(1P36.11) WILD-TYPE 225  84  55
D28V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          116                            225
  N1                           64                             84
  N2                           57                             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  1(1P36.11) MUTATED   160  46   6   0  24
  DEL PEAK  1(1P36.11) WILD-TYPE 286  28   4   2  39
D28V7, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           160                            286
  M1                            46                             28
  M1A                            6                              4
  M1B                            0                              2
  MX                            24                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   104 135
  DEL PEAK  1(1P36.11) WILD-TYPE 179 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    104  135
  DEL PEAK  1(1P36.11) WILD-TYPE  179  186
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                          104                            179
  MALE                            135                            186
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                    151
  DEL PEAK  1(1P36.11) WILD-TYPE                  227
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              11
  DEL PEAK  1(1P36.11) WILD-TYPE                            48
                                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
D28V9, multiclass
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            11
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      227
  COLON MUCINOUS ADENOCARCINOMA                              48
  RECTAL ADENOCARCINOMA                                      81
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     4 235
  DEL PEAK  1(1P36.11) WILD-TYPE   5 360
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      4  235
  DEL PEAK  1(1P36.11) WILD-TYPE    5  360
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             4                              5
  YES                          235                            360
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   162   2  21  12
  DEL PEAK  1(1P36.11) WILD-TYPE 274   3  15  17
D28V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          162                            274
  R1                            2                              3
  R2                           21                             15
  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                          21   115
  DEL PEAK  1(1P36.11) WILD-TYPE                        35   177
D28V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     115
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED   126  38
  DEL PEAK  2(1P33) WILD-TYPE 340  71
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        164                         411 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         38                          71 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       43.76        35.11        15.52        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 
       14.53        32.45        29.19        23.61        29.16        22.52 
TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       21.76        23.87         5.03        38.99         9.07        37.05 
TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 
        8.05        21.01        19.99        50.04        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       85.05         0.99        38.99        36.95        37.02         0.99 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 
       33.07        32.05        31.07        17.03        24.03         2.01 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F 
       12.99         2.01        21.99        13.05         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       42.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        22.03        41.00         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D 
        1.02         0.20         0.43        14.50        16.31         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.65         5.13        62.79        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 
        3.19         2.24         3.06         2.14         0.26         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
        8.02        13.02        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6924 TCGA-D5-6929 
       13.51         1.32        15.12        17.85        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A288 TCGA-DM-A28A 
       11.38        38.20        92.75        49.91        14.04        26.47 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       35.97        13.38         1.55        35.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       23.51        61.87        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV 
       46.75         4.11        10.98         5.98         5.49        26.99 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K 
       24.13        17.23        13.55        14.50        15.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 
       65.98        11.84        32.02         1.02        24.00        34.03 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       29.98         1.02        19.99         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       28.04        36.03        25.97        23.01        12.00        70.03 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
        1.94        38.96        38.04         0.49         0.69        10.19 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        13.97        10.98        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 
       13.97        36.00        30.05       126.44       129.27         0.49 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
       20.55        15.85        13.64        11.97        14.86         1.02 
TCGA-F5-6813 TCGA-G5-6572 
        0.69        47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       17.79        42.28        44.91        45.60        13.94        37.05 
TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       34.65        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
        1.02        24.03        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 
        1.02        17.98        15.95        14.93        17.03        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        39.98         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        0.10         0.76         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        61.41        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       11.74         1.94         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.01        12.03        14.99        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 
       20.19        20.42        17.75        18.25         7.92         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D7 
       12.00        10.26       119.70        24.43       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28         0.53        19.43       107.67        28.21 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        43.07        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.59         1.32         5.19        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       30.28        67.00        17.95        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       37.74        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         8.02         7.07         2.01         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        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-4022 
       14.01        32.02        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98        13.94         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       49.97        61.97        41.00         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.05         6.97        60.03         7.99 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02         7.10        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39         0.66         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     129.27                      140.38 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     15.945                      18.050 
[1] "0.2 - 129.3 (15.9)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   119  51
  DEL PEAK  2(1P33) WILD-TYPE 319 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    119   51
  DEL PEAK  2(1P33) WILD-TYPE  319  111
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  COLON                        119                         319
  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        49         1
  DEL PEAK  2(1P33) WILD-TYPE      83        1       29       122         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         7          5         24
  DEL PEAK  2(1P33) WILD-TYPE         3        19         16         54
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           20       28         6         0
  DEL PEAK  2(1P33) WILD-TYPE         33       33        21         2
D29V4, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           19                          83
  STAGE IA                           0                           1
  STAGE II                           7                          29
  STAGE IIA                         49                         122
  STAGE IIB                          1                           9
  STAGE IIC                          0                           3
  STAGE III                          7                          19
  STAGE IIIA                         5                          16
  STAGE IIIB                        24                          54
  STAGE IIIC                        20                          33
  STAGE IV                          28                          33
  STAGE IVA                          6                          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  2(1P33) MUTATED     4  23 124  20
  DEL PEAK  2(1P33) WILD-TYPE  16  82 288  45
D29V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         4                          16
  T2                        23                          82
  T3                       124                         288
  T4                        20                          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  2(1P33) MUTATED    82  50  39
  DEL PEAK  2(1P33) WILD-TYPE 259  98  73
D29V6, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        82                         259
  N1                        50                          98
  N2                        39                          73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  2(1P33) MUTATED   116  32   2   0  20
  DEL PEAK  2(1P33) WILD-TYPE 330  42   8   2  43
D29V7, multiclass
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  M0                        116                         330
  M1                         32                          42
  M1A                         2                           8
  M1B                         0                           2
  MX                         20                          43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    78  94
  DEL PEAK  2(1P33) WILD-TYPE 205 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     78   94
  DEL PEAK  2(1P33) WILD-TYPE  205  227
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        78                         205
  MALE                          94                         227
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                    109
  DEL PEAK  2(1P33) WILD-TYPE                  269
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                              10
  DEL PEAK  2(1P33) WILD-TYPE                            49
                             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
D29V9, multiclass
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                 109
  COLON MUCINOUS ADENOCARCINOMA                         10
  RECTAL ADENOCARCINOMA                                 49
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                   269
  COLON MUCINOUS ADENOCARCINOMA                           49
  RECTAL ADENOCARCINOMA                                   97
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     3 169
  DEL PEAK  2(1P33) WILD-TYPE   6 426
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3  169
  DEL PEAK  2(1P33) WILD-TYPE    6  426
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          3                           6
  YES                       169                         426
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED   113   2  14   8
  DEL PEAK  2(1P33) WILD-TYPE 323   3  22  21
D29V11, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                       113                         323
  R1                         2                           3
  R2                        14                          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"
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                          20    83
  DEL PEAK  2(1P33) WILD-TYPE                        36   209
D29V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               20
  WHITE                                                   83
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 36
  WHITE                                                    209
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.2) MUTATED   127  37
  DEL PEAK  3(1P13.2) WILD-TYPE 339  72
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          164                           411 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           37                            72 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3810 
       37.02        43.76        35.11        15.52        37.25        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 
       14.53        32.45        29.19        23.61        22.52        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       23.87        52.44         5.03        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 
       37.05        21.01        13.94        19.99        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 
       19.00         0.99        38.99        37.02         0.99        32.05 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 
       31.07        17.03        24.03         2.01        12.99         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q 
        2.01        21.99        13.05         7.96        38.04        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X 
       15.02        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        41.00        40.96         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D 
        1.02         0.20         0.43         0.92        14.50         5.52 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
        5.65        32.94         5.13        65.00        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 
        5.23         3.19         2.24         3.06         2.14         0.26 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 
        2.01         8.02        13.02        22.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 
       13.02        15.02        11.08        10.06        13.51        17.75 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
        1.32        15.12        14.30        13.41        11.38        92.75 
TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 
       49.91       131.51         6.12        14.04        26.47        13.38 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
        1.55        16.24        33.67        35.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       23.51        61.87        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 
        4.11        10.98         5.98         5.49        26.99        24.13 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AF-A56N 
       17.23        13.55        14.50        15.39        65.98        11.84 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3728 
       32.02         1.02        24.00        34.03         2.01        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        19.99         1.02        19.99        28.04        36.03 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A032 
       25.97        23.01        12.00        70.03         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 
        0.49         0.69        10.19         9.37        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE 
       13.97        36.00        30.05       126.44        41.36       129.27 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 TCGA-EI-6885 
        0.49        20.55        17.00        15.85        11.51        13.64 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       11.97        14.86         1.02         0.66         0.69         0.76 
TCGA-G5-6233 TCGA-G5-6572 
       18.28        47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 
       42.28        44.91        45.60        13.94        37.05        16.04 
TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       34.65        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
        1.02        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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        36.95        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
       33.07        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 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-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         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.10         0.76         0.46        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25        50.37        58.39         1.41        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 
       62.79        61.41        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 
        1.94         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       48.20        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-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        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       19.59        11.51        20.19        20.42        18.25         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-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        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       29.59         1.28         0.53        19.43       107.67        28.21 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        43.07        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        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        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        2.79         5.59         1.32         5.19        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 
       14.76        30.28        67.00        17.95        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       12.72        37.74        10.39         8.45        20.02        10.39 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       86.63        36.03        12.00         8.02         7.07         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       15.95        19.99        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 
       35.01        14.01        48.03        32.02        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
       17.03         0.99        20.98        13.94         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-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.97        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.72         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02         7.10        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       10.06         5.29        57.24        24.13        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
        2.40        19.96        20.91        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 
       16.31        16.41         8.61        10.78        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        9.96        37.51        31.30         0.39         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.46        55.76        26.43 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       15.455                        18.050 
[1] "0.2 - 131.5 (15.5)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D30V2, continuous
D30V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   117  52
  DEL PEAK  3(1P13.2) WILD-TYPE 321 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    117   52
  DEL PEAK  3(1P13.2) WILD-TYPE  321  110
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  COLON                          117                           321
  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        47         1
  DEL PEAK  3(1P13.2) WILD-TYPE      83        1       28       124         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.2) MUTATED           2         5          4         23
  DEL PEAK  3(1P13.2) WILD-TYPE         1        21         17         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.2) MUTATED           21       29         6         0
  DEL PEAK  3(1P13.2) WILD-TYPE         32       32        21         2
D30V4, multiclass
            clus
vv           DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  STAGE I                             19                            83
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           47                           124
  STAGE IIB                            1                             9
  STAGE IIC                            2                             1
  STAGE III                            5                            21
  STAGE IIIA                           4                            17
  STAGE IIIB                          23                            55
  STAGE IIIC                          21                            32
  STAGE IV                            29                            32
  STAGE IVA                            6                            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  3(1P13.2) MUTATED     5  21 123  21
  DEL PEAK  3(1P13.2) WILD-TYPE  15  84 289  44
D30V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           5                            15
  T2                          21                            84
  T3                         123                           289
  T4                          21                            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  3(1P13.2) MUTATED    81  45  44
  DEL PEAK  3(1P13.2) WILD-TYPE 260 103  68
D30V6, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          81                           260
  N1                          45                           103
  N2                          44                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  3(1P13.2) MUTATED   117  34   1   0  17
  DEL PEAK  3(1P13.2) WILD-TYPE 329  40   9   2  46
D30V7, multiclass
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  M0                          117                           329
  M1                           34                            40
  M1A                           1                             9
  M1B                           0                             2
  MX                           17                            46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED    77  94
  DEL PEAK  3(1P13.2) WILD-TYPE 206 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     77   94
  DEL PEAK  3(1P13.2) WILD-TYPE  206  227
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          77                           206
  MALE                            94                           227
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                    107
  DEL PEAK  3(1P13.2) WILD-TYPE                  271
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                              10
  DEL PEAK  3(1P13.2) WILD-TYPE                            49
                               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
D30V9, multiclass
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  COLON ADENOCARCINOMA                                   107
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     271
  COLON MUCINOUS ADENOCARCINOMA                             49
  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"
D30V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     4 167
  DEL PEAK  3(1P13.2) WILD-TYPE   5 428
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      4  167
  DEL PEAK  3(1P13.2) WILD-TYPE    5  428
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                            4                             5
  YES                         167                           428
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.2) MUTATED   114   1  14   9
  DEL PEAK  3(1P13.2) WILD-TYPE 322   4  22  20
D30V11, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                         114                           322
  R1                           1                             4
  R2                          14                            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"
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                          19    85
  DEL PEAK  3(1P13.2) WILD-TYPE                        37   207
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     85
                                  clus
vv                                 DEL PEAK  3(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    16   3
  DEL PEAK  4(2P12) WILD-TYPE 450 106
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         19                         556 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          3                         106 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-A6-2677 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 TCGA-AA-A01S 
       17.79         6.97        19.99        37.02        12.99         1.02 
TCGA-CM-5341 TCGA-G4-6626 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       29.06        46.75        15.39        32.02         1.02         6.05 
TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-A00H TCGA-AG-A02X TCGA-DC-6156 
       19.99         1.02        28.04        25.97        41.00        15.02 
TCGA-F5-6571 
       31.30 

$`DEL PEAK  4(2P12) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-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-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        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 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01        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         4.21        56.55         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.20        21.44        17.82         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50         8.45        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-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        12.00        13.97        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                       1.02                        0.07 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      46.75                      140.38 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                     19.990                      17.785 
[1] "1.0 - 46.8 (20.0)"  "0.1 - 140.4 (17.8)"
[1] "hr=" "1"  
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8  13
  DEL PEAK  4(2P12) WILD-TYPE 430 149
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   13
  DEL PEAK  4(2P12) WILD-TYPE  430  149
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  COLON                          8                         430
  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     100        1       35       164        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         19         77
                             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         48       60        26         2
D31V4, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                         100
  STAGE IA                           0                           1
  STAGE II                           1                          35
  STAGE IIA                          7                         164
  STAGE IIB                          0                          10
  STAGE IIC                          0                           3
  STAGE III                          1                          25
  STAGE IIIA                         2                          19
  STAGE IIIB                         1                          77
  STAGE IIIC                         5                          48
  STAGE IV                           1                          60
  STAGE IVA                          1                          26
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  4(2P12) MUTATED     0   4  15   2
  DEL PEAK  4(2P12) WILD-TYPE  20 101 397  63
D31V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                          20
  T2                         4                         101
  T3                        15                         397
  T4                         2                          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  4(2P12) MUTATED    10   5   6
  DEL PEAK  4(2P12) WILD-TYPE 331 143 106
D31V6, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        10                         331
  N1                         5                         143
  N2                         6                         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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  4(2P12) MUTATED    18   1   1   0   1
  DEL PEAK  4(2P12) WILD-TYPE 428  73   9   2  62
D31V7, multiclass
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  M0                         18                         428
  M1                          1                          73
  M1A                         1                           9
  M1B                         0                           2
  MX                          1                          62
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11  10
  DEL PEAK  4(2P12) WILD-TYPE 272 311
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11   10
  DEL PEAK  4(2P12) WILD-TYPE  272  311
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                        11                         272
  MALE                          10                         311
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      8
  DEL PEAK  4(2P12) WILD-TYPE                  370
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                               0
  DEL PEAK  4(2P12) WILD-TYPE                            59
                             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
D31V9, multiclass
                                clus
vv                               DEL PEAK  4(2P12) MUTATED
  COLON ADENOCARCINOMA                                   8
  COLON MUCINOUS ADENOCARCINOMA                          0
  RECTAL ADENOCARCINOMA                                 11
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  4(2P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   370
  COLON MUCINOUS ADENOCARCINOMA                           59
  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"
D31V10, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     1  20
  DEL PEAK  4(2P12) WILD-TYPE   8 575
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      1   20
  DEL PEAK  4(2P12) WILD-TYPE    8  575
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          1                           8
  YES                        20                         575
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P12) MUTATED    18   0   1   0
  DEL PEAK  4(2P12) WILD-TYPE 418   5  35  29
D31V11, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        18                         418
  R1                         0                           5
  R2                         1                          35
  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                        56   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                                 56
  WHITE                                                    286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    25   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 441 102
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           32                           543 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                           102 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3522 
       42.28        36.53        21.76        24.92         6.97        37.05 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3848 
       19.99         2.01        15.02         0.99        37.02         0.99 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AZ-4308 TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 
       12.99        24.00        75.25         2.24         3.29        49.91 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6626 TCGA-AF-A56L 
       44.32       131.51       117.07         1.55        46.75        65.98 
TCGA-AG-3609 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A02X TCGA-DC-6682 
       19.99        36.03        25.97        15.95        41.00        13.05 
TCGA-F5-6571 TCGA-F5-6814 
       31.30         0.53 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        17.79        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        34.65        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 
       15.95        38.99        36.95        14.93        17.03        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52         6.87        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32         7.92        15.12        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
       26.47        81.37       119.93        35.97        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       14.76        30.28        67.00        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50         8.45        15.39        20.02        10.39        86.63 
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-3587 TCGA-AG-3593 
        1.02         2.01        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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       20.98        13.94         6.02        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         0.53                          0.07 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                        24.46                         17.56 
[1] "0.5 - 131.5 (24.5)" "0.1 - 140.4 (17.6)"
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    24  11
  DEL PEAK  5(2Q22.1) WILD-TYPE 414 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     24   11
  DEL PEAK  5(2Q22.1) WILD-TYPE  414  151
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON                           24                           414
  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     100        1       35       156        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         20         74
                               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         46       59        26         2
D32V4, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              2                           100
  STAGE IA                             0                             1
  STAGE II                             1                            35
  STAGE IIA                           15                           156
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           1                            20
  STAGE IIIB                           4                            74
  STAGE IIIC                           7                            46
  STAGE IV                             2                            59
  STAGE IVA                            1                            26
  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  20 101 385  61
D32V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           101
  T3                          27                           385
  T4                           4                            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  5(2Q22.1) MUTATED    18   8   9
  DEL PEAK  5(2Q22.1) WILD-TYPE 323 140 103
D32V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          18                           323
  N1                           8                           140
  N2                           9                           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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  5(2Q22.1) MUTATED    30   2   1   0   2
  DEL PEAK  5(2Q22.1) WILD-TYPE 416  72   9   2  61
D32V7, multiclass
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  M0                           30                           416
  M1                            2                            72
  M1A                           1                             9
  M1B                           0                             2
  MX                            2                            61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    15  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 268 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     15   20
  DEL PEAK  5(2Q22.1) WILD-TYPE  268  301
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          15                           268
  MALE                            20                           301
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                     21
  DEL PEAK  5(2Q22.1) WILD-TYPE                  357
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                               3
  DEL PEAK  5(2Q22.1) WILD-TYPE                            56
                               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
D32V9, 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                                     357
  COLON MUCINOUS ADENOCARCINOMA                             56
  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"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  35
  DEL PEAK  5(2Q22.1) WILD-TYPE   9 560
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   35
  DEL PEAK  5(2Q22.1) WILD-TYPE    9  560
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                            0                             9
  YES                          35                           560
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q22.1) MUTATED    25   0   2   2
  DEL PEAK  5(2Q22.1) WILD-TYPE 411   5  34  27
D32V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          25                           411
  R1                           0                             5
  R2                           2                            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"
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                        54   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                                   54
  WHITE                                                      280
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  6(3P26.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.3) MUTATED    69  17
  DEL PEAK  6(3P26.3) WILD-TYPE 397  92
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           86                           489 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           17                            92 
$`DEL PEAK  6(3P26.3) MUTATED`
TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       43.43        15.52        34.65        36.53        14.53        32.45 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 
       29.16        22.52        25.08        21.76         9.63         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3662 TCGA-AA-3679 
        6.97        38.99         9.07        29.00         6.05        15.02 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3870 
       85.05         0.99        32.05        31.07        17.03        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
        2.01        12.99         2.01         2.01        21.99        50.99 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01K 
       24.00         7.96        13.94        27.02        32.02        31.00 
TCGA-AA-A02H TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 
        2.01         0.43         0.20         5.65         5.13        12.10 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
        3.19         3.29         0.26         2.01         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 
       29.06        22.03         5.03        14.04        11.08        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        17.75         1.32         7.92        15.12        17.85 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV 
       13.41        11.38         7.50        13.38         5.98        26.99 
TCGA-RU-A8FL TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 
       30.28        13.55        12.72        14.50         2.01        24.00 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-A02N TCGA-AH-6544 TCGA-BM-6198 
        0.99         1.02        19.99        61.97         0.49        10.19 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6512 TCGA-EI-6514 
        6.05         4.73        13.05         5.29        17.69        16.31 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`DEL PEAK  6(3P26.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.05        37.25        16.04        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13         8.38        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-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-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        24.03        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       16.08        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        8.02        26.04        27.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       11.51        20.42        18.25         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       52.80         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       67.00        24.13        17.95        17.23        43.04        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        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-3586 TCGA-AG-3587 TCGA-AG-3593 
        8.02         7.07         1.02         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         7.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-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-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        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-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-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        1.81         6.05         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-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-6513 TCGA-EI-6881 
       20.91        17.00        18.28        15.85        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                       13.395                        19.070 
[1] "0.2 - 85.0 (13.4)"  "0.1 - 140.4 (19.1)"
[1] "hr=" "1.6"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    68  20
  DEL PEAK  6(3P26.3) WILD-TYPE 370 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     68   20
  DEL PEAK  6(3P26.3) WILD-TYPE  370  142
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  COLON                           68                           370
  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        24         0
  DEL PEAK  6(3P26.3) WILD-TYPE      94        1       33       147        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         19         64
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(3P26.3) MUTATED            8       19         5         0
  DEL PEAK  6(3P26.3) WILD-TYPE         45       42        22         2
D33V4, multiclass
            clus
vv           DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  STAGE I                              8                            94
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           24                           147
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           2                            19
  STAGE IIIB                          14                            64
  STAGE IIIC                           8                            45
  STAGE IV                            19                            42
  STAGE IVA                            5                            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  6(3P26.3) MUTATED     2   8  69  11
  DEL PEAK  6(3P26.3) WILD-TYPE  18  97 343  54
D33V5, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  T1                           2                            18
  T2                           8                            97
  T3                          69                           343
  T4                          11                            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  6(3P26.3) MUTATED    38  28  24
  DEL PEAK  6(3P26.3) WILD-TYPE 303 120  88
D33V6, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  N0                          38                           303
  N1                          28                           120
  N2                          24                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  6(3P26.3) MUTATED    55  21   3   0   9
  DEL PEAK  6(3P26.3) WILD-TYPE 391  53   7   2  54
D33V7, multiclass
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  M0                           55                           391
  M1                           21                            53
  M1A                           3                             7
  M1B                           0                             2
  MX                            9                            54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    40  50
  DEL PEAK  6(3P26.3) WILD-TYPE 243 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     40   50
  DEL PEAK  6(3P26.3) WILD-TYPE  243  271
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  FEMALE                          40                           243
  MALE                            50                           271
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                     64
  DEL PEAK  6(3P26.3) WILD-TYPE                  314
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                               4
  DEL PEAK  6(3P26.3) WILD-TYPE                            55
                               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
D33V9, multiclass
                                clus
vv                               DEL PEAK  6(3P26.3) MUTATED
  COLON ADENOCARCINOMA                                    64
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   16
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  6(3P26.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     314
  COLON MUCINOUS ADENOCARCINOMA                             55
  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"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED     2  88
  DEL PEAK  6(3P26.3) WILD-TYPE   7 507
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED      2   88
  DEL PEAK  6(3P26.3) WILD-TYPE    7  507
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  NO                            2                             7
  YES                          88                           507
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P26.3) MUTATED    61   0  11   5
  DEL PEAK  6(3P26.3) WILD-TYPE 375   5  25  24
D33V11, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  R0                          61                           375
  R1                           0                             5
  R2                          11                            25
  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                           7    44
  DEL PEAK  6(3P26.3) WILD-TYPE                        49   248
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  6(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     44
                                  clus
vv                                 DEL PEAK  6(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      248
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  7(3P14.2) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.2) MUTATED    89  21
  DEL PEAK  7(3P14.2) WILD-TYPE 377  88
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          110                           465 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           21                            88 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-4T-AA8H TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
        5.26        15.52        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 
       32.45        29.16        22.52        25.08        21.76        20.12 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       52.44         9.63         5.03        38.99         1.02         9.07 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3697 
        6.05        54.02         0.92        11.01        37.05        85.05 
TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3939 
        0.99        32.05        31.07        17.03         2.01        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
        2.01        21.99        24.00        27.02         7.96        13.94 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K 
       18.05        17.03        27.02         0.99        32.02        31.00 
TCGA-AA-A02W TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       41.00        21.37         0.79         1.58         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-6600 
       14.50        16.31         0.20        75.25         5.65        12.10 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        3.29         0.26         2.01         8.02         5.03        14.04 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       14.04        13.05        11.08        11.01        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 
        1.32         7.92        17.85        13.41        11.38       119.70 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 TCGA-NH-A6GA 
        7.50        35.97       117.07        13.38        36.00         5.98 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2693 
        5.49        26.99        30.28        67.00        43.04        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3580 TCGA-AG-3581 
       12.72        14.50        86.63        11.84         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-4007 
        2.01        24.00         1.02        32.98        19.99         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
       17.03         6.02        38.96         0.49        10.19         6.05 
TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 
        9.37        15.02         7.10        13.05         5.29        20.91 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`DEL PEAK  7(3P14.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.05        37.25        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       61.84         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        15.02         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        53.00        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        26.01        25.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05         4.01        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       22.03        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.02         0.10         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52         6.87        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       19.59        13.51        11.51        20.42        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       11.64         1.51        12.00        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
       14.04        26.47        81.37       119.93        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 
        5.19        17.29         6.64        14.76        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.23        13.55        37.74        10.39         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        10.39        65.98        36.03        12.00        32.02 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        29.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        4.60         1.81         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        15.02        36.00        30.05        12.95        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        19.96        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       119.70                        140.38 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                        14.04                         19.07 
[1] "0.2 - 119.7 (14.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    85  29
  DEL PEAK  7(3P14.2) WILD-TYPE 353 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     85   29
  DEL PEAK  7(3P14.2) WILD-TYPE  353  133
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  COLON                           85                           353
  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        32         0
  DEL PEAK  7(3P14.2) WILD-TYPE      83        1       33       139        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         20         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P14.2) MUTATED           11       17         6         1
  DEL PEAK  7(3P14.2) WILD-TYPE         42       44        21         1
D34V4, multiclass
            clus
vv           DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  STAGE I                             19                            83
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           32                           139
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           1                            20
  STAGE IIIB                          18                            60
  STAGE IIIC                          11                            42
  STAGE IV                            17                            44
  STAGE IVA                            6                            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  7(3P14.2) MUTATED     7  15  78  16
  DEL PEAK  7(3P14.2) WILD-TYPE  13  90 334  49
D34V5, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                           7                            13
  T2                          15                            90
  T3                          78                           334
  T4                          16                            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  7(3P14.2) MUTATED    58  31  27
  DEL PEAK  7(3P14.2) WILD-TYPE 283 117  85
D34V6, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                          58                           283
  N1                          31                           117
  N2                          27                            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  7(3P14.2) MUTATED    76  20   3   1  14
  DEL PEAK  7(3P14.2) WILD-TYPE 370  54   7   1  49
D34V7, multiclass
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  M0                           76                           370
  M1                           20                            54
  M1A                           3                             7
  M1B                           1                             1
  MX                           14                            49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    51  65
  DEL PEAK  7(3P14.2) WILD-TYPE 232 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     51   65
  DEL PEAK  7(3P14.2) WILD-TYPE  232  256
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                          51                           232
  MALE                            65                           256
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                     76
  DEL PEAK  7(3P14.2) WILD-TYPE                  302
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                               9
  DEL PEAK  7(3P14.2) WILD-TYPE                            50
                               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
D34V9, multiclass
                                clus
vv                               DEL PEAK  7(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                    76
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   25
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  7(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     302
  COLON MUCINOUS ADENOCARCINOMA                             50
  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"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED     2 114
  DEL PEAK  7(3P14.2) WILD-TYPE   7 481
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      2  114
  DEL PEAK  7(3P14.2) WILD-TYPE    7  481
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  NO                            2                             7
  YES                         114                           481
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P14.2) MUTATED    80   1  11   5
  DEL PEAK  7(3P14.2) WILD-TYPE 356   4  25  24
D34V11, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  R0                          80                           356
  R1                           1                             4
  R2                          11                            25
  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                          14    53
  DEL PEAK  7(3P14.2) WILD-TYPE                        42   239
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK  7(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK  8(3Q26.31) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(3Q26.31) MUTATED    49  12
  DEL PEAK  8(3Q26.31) WILD-TYPE 417  97
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            61                            514 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            12                             97 
$`DEL PEAK  8(3Q26.31) MUTATED`
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3662 
       15.52        37.25        14.53        32.45        38.99         6.05 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       85.05         0.99        32.05        12.99         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01T TCGA-AD-6548 
        7.96        13.94        27.02        32.02        33.04        21.37 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CM-4752 
        1.58         0.43        15.75        12.10         0.26        13.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6529 
       15.02         5.03        11.08        11.01        13.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        1.32         7.92        17.85        13.41        12.00        11.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6297 TCGA-G4-6317 TCGA-QG-A5YV 
        7.50       131.51        35.97        82.39        36.00        26.99 
TCGA-RU-A8FL TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3599 
       30.28        12.72        14.50        32.02         2.01        12.03 
TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A02G TCGA-CI-6619 
       19.99         1.02        36.03        14.04        38.96         6.05 
TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-7002 
       13.05         5.29        19.96        20.91         8.61        11.97 
TCGA-G5-6233 
       18.28 

$`DEL PEAK  8(3Q26.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       13.94        37.05        16.04        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       34.03        18.05        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
        0.07         4.21        56.55         0.79         0.72         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        3.06         2.14         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 
       19.59        11.51        20.42        17.75        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       11.64         1.51        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       19.10        37.74        10.39         8.45        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-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         1.02        24.00         1.02        46.03 
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-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.97         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 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 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-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-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                          0.26                           0.07 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                         14.04                          18.05 
[1] "0.3 - 131.5 (14.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    44  17
  DEL PEAK  8(3Q26.31) WILD-TYPE 394 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     44   17
  DEL PEAK  8(3Q26.31) WILD-TYPE  394  145
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON                            44                            394
  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        21         0
  DEL PEAK  8(3Q26.31) WILD-TYPE      97        1       35       150        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         21         72
                                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         44       49        23         2
D35V4, multiclass
            clus
vv           DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  STAGE I                               5                             97
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            21                            150
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             3                             23
  STAGE IIIA                            0                             21
  STAGE IIIB                            6                             72
  STAGE IIIC                            9                             44
  STAGE IV                             12                             49
  STAGE IVA                             4                             23
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  8(3Q26.31) MUTATED     0   6  47   9
  DEL PEAK  8(3Q26.31) WILD-TYPE  20  99 365  56
D35V5, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  T1                            0                             20
  T2                            6                             99
  T3                           47                            365
  T4                            9                             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  8(3Q26.31) MUTATED    30  14  18
  DEL PEAK  8(3Q26.31) WILD-TYPE 311 134  94
D35V6, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  N0                           30                            311
  N1                           14                            134
  N2                           18                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  8(3Q26.31) MUTATED    41  13   2   0   6
  DEL PEAK  8(3Q26.31) WILD-TYPE 405  61   8   2  57
D35V7, multiclass
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  M0                            41                            405
  M1                            13                             61
  M1A                            2                              8
  M1B                            0                              2
  MX                             6                             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    26  36
  DEL PEAK  8(3Q26.31) WILD-TYPE 257 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     26   36
  DEL PEAK  8(3Q26.31) WILD-TYPE  257  285
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  FEMALE                           26                            257
  MALE                             36                            285
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                     41
  DEL PEAK  8(3Q26.31) WILD-TYPE                  337
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                               3
  DEL PEAK  8(3Q26.31) WILD-TYPE                            56
                                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
D35V9, multiclass
                                clus
vv                               DEL PEAK  8(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                     41
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      337
  COLON MUCINOUS ADENOCARCINOMA                              56
  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"
D35V10, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED     1  61
  DEL PEAK  8(3Q26.31) WILD-TYPE   8 534
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED      1   61
  DEL PEAK  8(3Q26.31) WILD-TYPE    8  534
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  NO                             1                              8
  YES                           61                            534
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  8(3Q26.31) MUTATED    47   0   5   2
  DEL PEAK  8(3Q26.31) WILD-TYPE 389   5  31  27
D35V11, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  R0                           47                            389
  R1                            0                              5
  R2                            5                             31
  RX                            2                             27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                           7    31
  DEL PEAK  8(3Q26.31) WILD-TYPE                        49   261
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      31
                                  clus
vv                                 DEL PEAK  8(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    49
  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"

Clustering(36) Variable = DEL PEAK  9(4P16.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P16.2) MUTATED   142  40
  DEL PEAK  9(4P16.2) WILD-TYPE 324  69
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          182                           393 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                           40                            69 
$`DEL PEAK  9(4P16.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 
       37.05        16.04        14.53        32.45        30.44        29.16 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       25.18        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
        9.63         5.03         1.02        38.99        37.05        34.03 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 
       12.99        21.01        13.02        19.99         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
        2.01        50.04        15.02        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       29.98         2.01        12.99         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       21.99        50.99        26.01        34.03        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        2.01        41.00         1.58         1.02         0.20        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
        0.95        15.75         0.20         5.52         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 
       65.00        12.10        29.56         3.19         2.14         3.29 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5864 
       48.20         8.02        29.06        22.03        22.98        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 
       17.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.01        10.06        14.99        13.51        20.19        17.75 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA 
       14.30         9.04        13.41        11.38        12.59         7.50 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
        6.12        14.04        26.47         1.55        16.24        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
       35.41         8.35        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 
       46.75         4.11        10.98         5.49        26.99        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       17.23        43.04        12.72        37.74        14.50        15.39 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 
       10.39        65.98         1.02        46.03        34.03         6.05 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
       29.98         1.02        32.98         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       14.04        13.94        25.97        23.01        12.00        70.03 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        41.00         0.69        10.19         6.05         6.05 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        4.73        12.99        15.02        36.00         7.10        30.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 
      126.44       129.27        32.61         2.40        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.41        11.97         8.45        31.30        14.86         0.39 
TCGA-F5-6813 TCGA-G5-6641 
        0.69        26.43 

$`DEL PEAK  9(4P16.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       42.28        45.60        37.25        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       16.24        24.92         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 
       19.99        13.94        61.02        78.08         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       14.93        36.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        24.00        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       14.99        21.99        34.98        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.06        51.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        16.31        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77       100.01         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.08        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        11.51        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
        6.18        35.87        16.31        29.59         1.28         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        82.39        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.98         5.59         1.32         5.19        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       14.76        30.28        67.00        17.95        13.55        19.10 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       10.39         8.45        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         2.01        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-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4008 
       19.99        36.95        13.02        14.01         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        38.04         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.72         4.60         1.81         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       13.97        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        51.48         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       20.91        17.00        18.28        17.69        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        37.51 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                        17.03                         17.95 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.4"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   129  62
  DEL PEAK  9(4P16.2) WILD-TYPE 309 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    129   62
  DEL PEAK  9(4P16.2) WILD-TYPE  309  100
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  COLON                          129                           309
  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        27        0        7        47         2
  DEL PEAK  9(4P16.2) WILD-TYPE      75        1       29       124         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(4P16.2) MUTATED           0         6          9         23
  DEL PEAK  9(4P16.2) WILD-TYPE         3        20         12         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(4P16.2) MUTATED           23       33        12         0
  DEL PEAK  9(4P16.2) WILD-TYPE         30       28        15         2
D36V4, multiclass
            clus
vv           DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  STAGE I                             27                            75
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           47                           124
  STAGE IIB                            2                             8
  STAGE IIC                            0                             3
  STAGE III                            6                            20
  STAGE IIIA                           9                            12
  STAGE IIIB                          23                            55
  STAGE IIIC                          23                            30
  STAGE IV                            33                            28
  STAGE IVA                           12                            15
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(4P16.2) MUTATED     6  32 131  24
  DEL PEAK  9(4P16.2) WILD-TYPE  14  73 281  41
D36V5, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  T1                           6                            14
  T2                          32                            73
  T3                         131                           281
  T4                          24                            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  9(4P16.2) MUTATED    88  56  49
  DEL PEAK  9(4P16.2) WILD-TYPE 253  92  63
D36V6, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  N0                          88                           253
  N1                          56                            92
  N2                          49                            63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  9(4P16.2) MUTATED   127  37   5   0  19
  DEL PEAK  9(4P16.2) WILD-TYPE 319  37   5   2  44
D36V7, multiclass
     clus
vv    DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  M0                          127                           319
  M1                           37                            37
  M1A                           5                             5
  M1B                           0                             2
  MX                           19                            44
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED    82 111
  DEL PEAK  9(4P16.2) WILD-TYPE 201 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED     82  111
  DEL PEAK  9(4P16.2) WILD-TYPE  201  210
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  FEMALE                          82                           201
  MALE                           111                           210
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                    119
  DEL PEAK  9(4P16.2) WILD-TYPE                  259
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                              10
  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
D36V9, multiclass
                                clus
vv                               DEL PEAK  9(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                   119
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   57
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  9(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     259
  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"
D36V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED     9 184
  DEL PEAK  9(4P16.2) WILD-TYPE   0 411
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED      9  184
  DEL PEAK  9(4P16.2) WILD-TYPE    0  411
     clus
vv    DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  NO                            9                             0
  YES                         184                           411
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P16.2) MUTATED   140   0  16   6
  DEL PEAK  9(4P16.2) WILD-TYPE 296   5  20  23
D36V11, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  R0                         140                           296
  R1                           0                             5
  R2                          16                            20
  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                          16    91
  DEL PEAK  9(4P16.2) WILD-TYPE                        40   201
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  9(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK  9(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED   162  41
  DEL PEAK 10(4Q22.1) WILD-TYPE 304  68
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          203                           372 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           41                            68 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       37.05        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       29.16        24.16        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 
       52.44         9.63         5.03         1.02        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 
       38.99        37.05        34.03        29.00        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       13.02        19.99         6.05         2.01        50.04        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00         0.99         0.99        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       17.03         0.99        33.07         0.99        31.07        17.03 
TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        2.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q 
       50.99        26.01        24.00        27.02        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       17.03        15.02        32.02        26.01         2.96        39.98 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       41.00         1.58         1.02         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-4681 
        0.95         0.20         5.52         6.87         5.13        83.80 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 
       65.00        12.10        29.56         2.14         3.29         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      102.44        48.20         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
        5.03        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       15.02        11.01        13.05        11.08        11.01        14.99 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        20.19        17.75         1.32         7.92        15.12 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD 
       14.30         9.04        13.41        12.00        11.38        24.43 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
       12.59         7.50        44.32         6.12        14.04        35.97 
TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       13.38        16.24        33.67        35.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 
       82.39        23.51        45.11        36.72        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL 
        4.11        10.98         5.98         5.49        26.99        30.28 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3593 
       37.74        14.50        15.39        65.98         1.02        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 
        6.05        19.99        29.98        32.98         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       17.03        13.94         6.02        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
       70.03        64.01         1.94        41.00         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
       10.19         6.05         6.05         4.73        11.01        12.99 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA 
       15.02        36.00         7.10        30.05        13.05       126.44 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
      129.27         2.40        20.91        17.00        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.41        11.97         8.45        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       42.28        45.60        37.25        16.04        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       20.61        24.69        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.92         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       58.03         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3538 
       36.03         8.05        19.07        19.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       12.99         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       17.98        15.95        14.93        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3971 
       12.99        24.00        33.01        26.01        24.00        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       17.03         4.01        27.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        39.06        51.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
        0.43         0.46         0.92        27.09        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.19        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02         8.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       16.04        21.99        14.99        12.99        14.04        12.95 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        10.06        12.03        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.44        11.64         1.51        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       29.59         1.28         0.53        19.43       107.67        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       13.78        35.80        26.17        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        2.79         5.59         1.32         5.19        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       14.76        67.00        17.95        10.39         8.45        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        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         2.01        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99         1.02         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-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.98        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
        1.02        31.00        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        38.04         1.45         0.72         4.60         1.81 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        60.03         7.99        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.02        12.00        13.97        12.95        10.06         5.29 
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-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       20.55        19.96        18.28        17.69        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        37.51 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        17.03                         18.05 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   141  70
  DEL PEAK 10(4Q22.1) WILD-TYPE 297  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    141   70
  DEL PEAK 10(4Q22.1) WILD-TYPE  297   92
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON                          141                           297
  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        25        0       11        57         2
  DEL PEAK 10(4Q22.1) WILD-TYPE      77        1       25       114         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4Q22.1) MUTATED           1         5          9         35
  DEL PEAK 10(4Q22.1) WILD-TYPE         2        21         12         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4Q22.1) MUTATED           27       26        11         1
  DEL PEAK 10(4Q22.1) WILD-TYPE         26       35        16         1
D37V4, multiclass
            clus
vv           DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  STAGE I                             25                            77
  STAGE IA                             0                             1
  STAGE II                            11                            25
  STAGE IIA                           57                           114
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           9                            12
  STAGE IIIB                          35                            43
  STAGE IIIC                          27                            26
  STAGE IV                            26                            35
  STAGE IVA                           11                            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 10(4Q22.1) MUTATED     6  28 154  27
  DEL PEAK 10(4Q22.1) WILD-TYPE  14  77 258  38
D37V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                           6                            14
  T2                          28                            77
  T3                         154                           258
  T4                          27                            38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 10(4Q22.1) MUTATED    99  64  52
  DEL PEAK 10(4Q22.1) WILD-TYPE 242  84  60
D37V6, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                          99                           242
  N1                          64                            84
  N2                          52                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 10(4Q22.1) MUTATED   150  31   5   1  23
  DEL PEAK 10(4Q22.1) WILD-TYPE 296  43   5   1  40
D37V7, multiclass
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  M0                          150                           296
  M1                           31                            43
  M1A                           5                             5
  M1B                           1                             1
  MX                           23                            40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    91 124
  DEL PEAK 10(4Q22.1) WILD-TYPE 192 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     91  124
  DEL PEAK 10(4Q22.1) WILD-TYPE  192  197
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          91                           192
  MALE                           124                           197
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                    131
  DEL PEAK 10(4Q22.1) WILD-TYPE                  247
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              10
  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
D37V9, multiclass
                                clus
vv                               DEL PEAK 10(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   131
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     247
  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"
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     8 207
  DEL PEAK 10(4Q22.1) WILD-TYPE   1 388
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      8  207
  DEL PEAK 10(4Q22.1) WILD-TYPE    1  388
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                            8                             1
  YES                         207                           388
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED   158   2  12   8
  DEL PEAK 10(4Q22.1) WILD-TYPE 278   3  24  21
D37V11, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                         158                           278
  R1                           2                             3
  R2                          12                            24
  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                          22   109
  DEL PEAK 10(4Q22.1) WILD-TYPE                        34   183
D37V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  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"

Clustering(38) Variable = DEL PEAK 11(4Q35.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.1) MUTATED   171  40
  DEL PEAK 11(4Q35.1) WILD-TYPE 295  69
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          211                           364 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           40                            69 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 
       37.05        37.25        34.65        32.45        29.19        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       22.52        24.13        24.16        20.61        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       20.28        61.84        52.44         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 
       38.99        37.05        34.03        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       33.99        21.01        13.02        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       54.02         2.01        50.04        37.05        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
        0.99        38.99        36.95        37.02        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 
       33.07        36.03         0.99        31.07        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       26.01        24.00         7.96        34.03        17.03        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01X 
       15.02        32.02        31.00        35.01         1.02        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
        2.96        39.98         2.01        41.00         1.02         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 
       14.50        16.31         0.95         0.20         5.52        75.25 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 
        5.65         5.13        65.00        12.10        29.56         2.24 
TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 
        2.14         0.10         1.35        48.20         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.01        11.08        11.01        14.99        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 
       17.75         1.32         7.92        17.85         7.53         9.04 
TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.41        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 
        6.12        14.04        26.47        13.38         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 
       33.67        35.41         8.35        82.39        23.51        45.11 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       36.72        91.79        46.75         4.11        10.98         5.98 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 
        1.32         5.49        26.99        30.28        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        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       14.50        15.39        65.98         1.02        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 
        6.05        19.99        29.98        32.98         0.99         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 
       48.03        19.99        28.04        36.03        14.04        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X 
       25.97        23.01        12.00        70.03        64.01        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
        0.49         0.69        10.19         6.05         6.05         4.73 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       11.01        12.99        15.02        36.00         7.10        30.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 
      126.44       129.27        24.13         2.40        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       16.34        16.41        11.97         9.96        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6864 TCGA-G5-6233 
        0.39         1.02         0.66         0.53         0.46        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 11(4Q35.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       42.28        44.91        16.04        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 
       32.71        27.09         8.38        25.08        25.18        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 
       24.39        20.12        19.66        16.24        24.92         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 
       36.03         8.05        19.07        19.07        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
        0.99        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       19.99        13.94        61.02         6.97        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3855 
       25.02         1.02        17.98        15.95        14.93        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
        2.01        13.05        34.06        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.72         1.58         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        15.75        21.44        17.82         5.19 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
        6.87        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         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         0.26         0.33        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 
        8.02        26.04        27.02        16.01        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        11.51        20.42        18.25        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 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        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       35.87        16.31        29.59         1.28         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      107.67        28.21        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        51.75        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F7 
       47.15        52.80        10.52         2.79         5.59         5.19 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 
       17.29         6.64        14.76        67.00        17.95         8.45 
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         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        7.99         0.99         1.02         0.99        19.99        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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02        17.03         0.99        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       15.95        36.03         9.07         1.02        31.00        10.98 
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-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 
        1.45         0.72         4.60         1.81         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03         7.99        10.98        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       13.97        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 
       10.78        13.64        17.46         8.45        37.51         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        55.76        47.08 

  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                       17.750                        17.885 
[1] "0.1 - 140.4 (17.8)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   151  69
  DEL PEAK 11(4Q35.1) WILD-TYPE 287  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    151   69
  DEL PEAK 11(4Q35.1) WILD-TYPE  287   93
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON                          151                           287
  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        30        0        9        61         1
  DEL PEAK 11(4Q35.1) WILD-TYPE      72        1       27       110         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q35.1) MUTATED           1         9          8         32
  DEL PEAK 11(4Q35.1) WILD-TYPE         2        17         13         46
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q35.1) MUTATED           29       29        10         1
  DEL PEAK 11(4Q35.1) WILD-TYPE         24       32        17         1
D38V4, multiclass
            clus
vv           DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  STAGE I                             30                            72
  STAGE IA                             0                             1
  STAGE II                             9                            27
  STAGE IIA                           61                           110
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            9                            17
  STAGE IIIA                           8                            13
  STAGE IIIB                          32                            46
  STAGE IIIC                          29                            24
  STAGE IV                            29                            32
  STAGE IVA                           10                            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 11(4Q35.1) MUTATED     7  33 159  25
  DEL PEAK 11(4Q35.1) WILD-TYPE  13  72 253  40
D38V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                           7                            13
  T2                          33                            72
  T3                         159                           253
  T4                          25                            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 11(4Q35.1) MUTATED   106  63  55
  DEL PEAK 11(4Q35.1) WILD-TYPE 235  85  57
D38V6, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                         106                           235
  N1                          63                            85
  N2                          55                            57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 11(4Q35.1) MUTATED   159  34   5   1  22
  DEL PEAK 11(4Q35.1) WILD-TYPE 287  40   5   1  41
D38V7, multiclass
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  M0                          159                           287
  M1                           34                            40
  M1A                           5                             5
  M1B                           1                             1
  MX                           22                            41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   105 119
  DEL PEAK 11(4Q35.1) WILD-TYPE 178 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    105  119
  DEL PEAK 11(4Q35.1) WILD-TYPE  178  202
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                         105                           178
  MALE                           119                           202
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                    136
  DEL PEAK 11(4Q35.1) WILD-TYPE                  242
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              15
  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
D38V9, multiclass
                                clus
vv                               DEL PEAK 11(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                   136
  COLON MUCINOUS ADENOCARCINOMA                           15
  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"
D38V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED     8 216
  DEL PEAK 11(4Q35.1) WILD-TYPE   1 379
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      8  216
  DEL PEAK 11(4Q35.1) WILD-TYPE    1  379
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                            8                             1
  YES                         216                           379
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q35.1) MUTATED   161   1  15   9
  DEL PEAK 11(4Q35.1) WILD-TYPE 275   4  21  20
D38V11, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         161                           275
  R1                           1                             4
  R2                          15                            21
  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                          24   109
  DEL PEAK 11(4Q35.1) WILD-TYPE                        32   183
D38V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 11(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      183
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED   110  35
  DEL PEAK 12(5Q12.1) WILD-TYPE 356  74
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          145                           430 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           35                            74 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        43.43        23.38        13.94        15.52 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 
       16.04        34.65        36.53        14.53        30.44        29.19 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3502 TCGA-AA-3538 TCGA-AA-3542 
       23.87         9.63         5.03        35.01        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       13.02        24.00        19.99        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 
       19.00        85.05         0.99        36.95        37.02        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3966 
        0.99        31.07        31.07        24.03         2.01         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       21.99        34.03        27.02        42.02         0.99        33.04 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        2.96         2.01        41.00         1.02         0.10         0.20 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31         0.20         5.65        65.00        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 
        5.23         1.94         3.29         1.35        48.20         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       14.04        29.03        13.02        17.75        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       10.13        12.43         9.04        44.32       131.51         6.12 
TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 
        8.61         1.55        33.67         8.35        82.39        45.11 
TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV 
       36.00        91.79         4.11        10.98         1.32        26.99 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 
        6.64        30.28        24.13        17.23        43.04        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3728 TCGA-AG-3731 
       10.39        15.39        10.39        86.63        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       32.98        19.99        17.03         1.02        48.03        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 
       36.03        17.03        23.01        70.03        64.01         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 
       38.96        41.00        10.19         6.05         7.99        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA 
       13.97        15.02        36.00         7.10        13.05       126.44 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 
       57.24       129.27        51.48        20.55        16.41        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6233 
       11.97         8.45        37.51        14.86         1.02        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
        5.06         5.26        46.65        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       35.11        45.60        37.05        37.25        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 
       29.16        22.52        24.13         8.38        20.61        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       36.03        32.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01        24.00        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         1.58         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.01       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
       12.49        16.14        15.58        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        51.75        39.42        35.93        36.72 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.59         5.19         5.49        17.29        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       17.95        13.55        19.10        12.72        14.50         8.45 
TCGA-AF-6655 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        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         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       14.01        32.02        19.99        14.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 
       36.03         9.07         1.02        12.00        31.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98        49.97        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         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        13.97        60.03        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.02        12.00        30.05        12.95        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6464 
       16.31         8.61        11.51        10.78        17.46         9.96 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        55.76        47.08 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       19.990                        17.375 
[1] "0.1 - 131.5 (20.0)" "0.1 - 140.4 (17.4)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   100  53
  DEL PEAK 12(5Q12.1) WILD-TYPE 338 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    100   53
  DEL PEAK 12(5Q12.1) WILD-TYPE  338  109
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON                          100                           338
  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        22        0        7        34         1
  DEL PEAK 12(5Q12.1) WILD-TYPE      80        1       29       137         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(5Q12.1) MUTATED           1         5          9         18
  DEL PEAK 12(5Q12.1) WILD-TYPE         2        21         12         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(5Q12.1) MUTATED           19       19        13         1
  DEL PEAK 12(5Q12.1) WILD-TYPE         34       42        14         1
D39V4, multiclass
            clus
vv           DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  STAGE I                             22                            80
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           34                           137
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           9                            12
  STAGE IIIB                          18                            60
  STAGE IIIC                          19                            34
  STAGE IV                            19                            42
  STAGE IVA                           13                            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 12(5Q12.1) MUTATED     5  26 105  17
  DEL PEAK 12(5Q12.1) WILD-TYPE  15  79 307  48
D39V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  T1                           5                            15
  T2                          26                            79
  T3                         105                           307
  T4                          17                            48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 12(5Q12.1) MUTATED    71  44  38
  DEL PEAK 12(5Q12.1) WILD-TYPE 270 104  74
D39V6, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  N0                          71                           270
  N1                          44                           104
  N2                          38                            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 12(5Q12.1) MUTATED   100  24   6   1  20
  DEL PEAK 12(5Q12.1) WILD-TYPE 346  50   4   1  43
D39V7, multiclass
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  M0                          100                           346
  M1                           24                            50
  M1A                           6                             4
  M1B                           1                             1
  MX                           20                            43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    68  85
  DEL PEAK 12(5Q12.1) WILD-TYPE 215 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     68   85
  DEL PEAK 12(5Q12.1) WILD-TYPE  215  236
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  FEMALE                          68                           215
  MALE                            85                           236
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                     92
  DEL PEAK 12(5Q12.1) WILD-TYPE                  286
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                               8
  DEL PEAK 12(5Q12.1) WILD-TYPE                            51
                               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
D39V9, multiclass
                                clus
vv                               DEL PEAK 12(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                    92
  COLON MUCINOUS ADENOCARCINOMA                            8
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     286
  COLON MUCINOUS ADENOCARCINOMA                             51
  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"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     8 145
  DEL PEAK 12(5Q12.1) WILD-TYPE   1 450
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      8  145
  DEL PEAK 12(5Q12.1) WILD-TYPE    1  450
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                            8                             1
  YES                         145                           450
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED   105   2   9   5
  DEL PEAK 12(5Q12.1) WILD-TYPE 331   3  27  24
D39V11, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                         105                           331
  R1                           2                             3
  R2                           9                            27
  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                          16    80
  DEL PEAK 12(5Q12.1) WILD-TYPE                        40   212
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     80
                                  clus
vv                                 DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   40
  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"

Clustering(40) Variable = DEL PEAK 13(5Q21.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q21.2) MUTATED   130  42
  DEL PEAK 13(5Q21.2) WILD-TYPE 336  67
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          172                           403 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                           42                            67 
$`DEL PEAK 13(5Q21.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       37.02        43.76        13.94        15.52        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       14.53        30.44        29.19        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A56B 
       25.18        24.16        21.76        23.87        20.28        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3538 
        9.63         5.03         1.02        37.05        19.07        26.01 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 
       12.99        13.02        24.00        19.99        61.02        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 
       47.01        15.02        11.01        19.00        85.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       36.95        37.02         0.99        33.07         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       31.07        17.03        24.03        24.00         2.01        21.99 
TCGA-AA-3994 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A01C 
       27.02        34.03        27.02        42.02        17.03        15.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
        0.99        33.04         2.96         2.01         5.03        41.00 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-6196 
        1.02         0.10         0.20         0.46        16.31         0.20 
TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       21.44         5.65        83.80        65.00        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 
        5.23         1.94         2.24         3.29         1.35        48.20 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 
        5.03        15.02        14.04        29.03        13.02        11.08 
TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 
       19.59        20.42        15.12        17.85        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB 
        9.04        13.41        11.38        92.75       140.38        44.32 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28K 
        7.76         6.12        14.04        26.47       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
        8.61        13.38         1.55        33.67         8.35        82.39 
TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC 
       45.11        36.00        91.79         4.11        10.98         1.32 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       26.99         6.64        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-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       32.02        19.99         7.99        29.98         1.02        32.98 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 
       19.99        17.03         1.02        48.03        28.04        36.03 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 
       17.03         6.02        23.01        70.03        64.01         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 
       38.96        41.00        10.19         6.05        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        36.00         7.10        13.05       126.44        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6885 
       51.48        20.55        18.28        16.34        16.41        13.64 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
        9.96        14.86         0.46        18.28 

$`DEL PEAK 13(5Q21.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        45.60        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       20.61        24.69        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92        61.84         1.02         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01         0.92        47.05         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 
       14.93        17.03        36.03        32.05        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-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         4.21        56.55         0.79         0.72         1.58 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.43         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 
       15.75        17.82         5.19         5.52         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       50.37        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 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         2.93         2.01 
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        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       12.00        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       20.19        17.75        18.25         1.32         7.92         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6924 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        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       55.04        51.75        39.42        35.93        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       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 
       47.15        52.80        10.52         2.79         5.98         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
        5.19         5.49        17.29        14.76        67.00        17.95 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        19.10        12.72        14.50         8.45        20.02 
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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99         0.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       35.01        14.01        32.02        19.99        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
        0.99        20.98        13.94        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 
       36.03         9.07         1.02        12.00        31.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98        49.97        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       11.01        15.02        12.00        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.29        41.36       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
        2.40        19.96        20.91        17.00        15.85        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                        18.64                         17.69 
[1] "0.1 - 140.4 (18.6)" "0.1 - 139.2 (17.7)"
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   127  55
  DEL PEAK 13(5Q21.2) WILD-TYPE 311 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    127   55
  DEL PEAK 13(5Q21.2) WILD-TYPE  311  107
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON                          127                           311
  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        24        0        8        40         1
  DEL PEAK 13(5Q21.2) WILD-TYPE      78        1       28       131         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q21.2) MUTATED           1         6         10         27
  DEL PEAK 13(5Q21.2) WILD-TYPE         2        20         11         51
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q21.2) MUTATED           23       23        14         1
  DEL PEAK 13(5Q21.2) WILD-TYPE         30       38        13         1
D40V4, multiclass
            clus
vv           DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  STAGE I                             24                            78
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           40                           131
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                          10                            11
  STAGE IIIB                          27                            51
  STAGE IIIC                          23                            30
  STAGE IV                            23                            38
  STAGE IVA                           14                            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 13(5Q21.2) MUTATED     4  30 127  21
  DEL PEAK 13(5Q21.2) WILD-TYPE  16  75 285  44
D40V5, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  T1                           4                            16
  T2                          30                            75
  T3                         127                           285
  T4                          21                            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 13(5Q21.2) MUTATED    81  56  45
  DEL PEAK 13(5Q21.2) WILD-TYPE 260  92  67
D40V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  N0                          81                           260
  N1                          56                            92
  N2                          45                            67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 13(5Q21.2) MUTATED   123  28   7   1  20
  DEL PEAK 13(5Q21.2) WILD-TYPE 323  46   3   1  43
D40V7, multiclass
     clus
vv    DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  M0                          123                           323
  M1                           28                            46
  M1A                           7                             3
  M1B                           1                             1
  MX                           20                            43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED    84  98
  DEL PEAK 13(5Q21.2) WILD-TYPE 199 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED     84   98
  DEL PEAK 13(5Q21.2) WILD-TYPE  199  223
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  FEMALE                          84                           199
  MALE                            98                           223
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                    114
  DEL PEAK 13(5Q21.2) WILD-TYPE                  264
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                              13
  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
D40V9, multiclass
                                clus
vv                               DEL PEAK 13(5Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   114
  COLON MUCINOUS ADENOCARCINOMA                           13
  RECTAL ADENOCARCINOMA                                   53
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     264
  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"
D40V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED     8 174
  DEL PEAK 13(5Q21.2) WILD-TYPE   1 421
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED      8  174
  DEL PEAK 13(5Q21.2) WILD-TYPE    1  421
     clus
vv    DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  NO                            8                             1
  YES                         174                           421
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.2) MUTATED   123   2  13   7
  DEL PEAK 13(5Q21.2) WILD-TYPE 313   3  23  22
D40V11, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  R0                         123                           313
  R1                           2                             3
  R2                          13                            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"
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                          17    91
  DEL PEAK 13(5Q21.2) WILD-TYPE                        39   201
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK 13(5Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      201
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 14(5Q22.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q22.2) MUTATED   129  43
  DEL PEAK 14(5Q22.2) WILD-TYPE 337  66
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          172                           403 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           43                            66 
$`DEL PEAK 14(5Q22.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       37.02        43.76        13.94        15.52        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       14.53        30.44        29.19        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.18        24.16        21.76        23.87         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
        1.02         1.02        37.05        19.07        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 TCGA-AA-3678 
       13.02        24.00        19.99        61.02        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3841 
       15.02        19.00        85.05        19.04         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02         0.99        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3986 TCGA-AA-A00F 
       24.03        24.00         2.01        21.99        19.07        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E 
       27.02        42.02        15.02         0.99        33.04         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        2.01         5.03        41.00         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 
        0.20        16.31         0.20        21.44         5.65        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
       65.00        62.79         6.77        29.56         5.23         1.94 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6751 TCGA-CM-4747 
        2.14         3.29         1.35        48.20       124.27         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       26.04         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        13.02        11.08        19.59        15.12 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       17.85        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A28A 
       92.75       140.38        44.32         7.76         6.12        26.47 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       60.79       117.07        98.24         8.61        13.38         1.55 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 
       33.67         8.35        82.39        45.11        36.00        91.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-RU-A8FL 
        4.11        10.98         1.32        26.99         6.64        30.28 
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-3612 TCGA-AG-3728 
       10.39        86.63        65.98        32.02        19.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
        1.02        32.98        19.99        17.03         1.02        48.03 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03        17.03         6.02        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 
       70.03        64.01         1.94        38.96        41.00         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.19         6.05         7.99        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       36.00         7.10        13.05       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 
       51.48        20.55        19.96        18.28        16.34        16.41 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
        9.96        14.86         0.46        18.28 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        45.60        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
        8.05        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        13.94        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       54.02         2.01        14.01         0.92        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
        5.98        37.05        36.00         5.03        26.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       38.99        14.93        17.03        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98        39.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72         1.58         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        15.75        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       32.94         5.13        22.36        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 
        2.93         2.01        23.05        20.02        37.02        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        14.99        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32         7.92         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58         7.53        12.39        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        49.91        13.32        12.59         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        46.75        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
        2.79         5.98         5.59         5.19         5.49        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       14.76        67.00        17.95        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        20.02        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         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
        1.02        31.00        10.98        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       10.98        11.01        15.02        12.00        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       10.06         5.29       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
        2.40        20.91        17.00        15.85        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                        18.64                         17.69 
[1] "0.1 - 140.4 (18.6)" "0.1 - 139.2 (17.7)"
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   125  59
  DEL PEAK 14(5Q22.2) WILD-TYPE 313 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    125   59
  DEL PEAK 14(5Q22.2) WILD-TYPE  313  103
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON                          125                           313
  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        25        0        9        44         0
  DEL PEAK 14(5Q22.2) WILD-TYPE      77        1       27       127        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q22.2) MUTATED           1         6          9         26
  DEL PEAK 14(5Q22.2) WILD-TYPE         2        20         12         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q22.2) MUTATED           22       23        13         1
  DEL PEAK 14(5Q22.2) WILD-TYPE         31       38        14         1
D41V4, multiclass
            clus
vv           DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  STAGE I                             25                            77
  STAGE IA                             0                             1
  STAGE II                             9                            27
  STAGE IIA                           44                           127
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           9                            12
  STAGE IIIB                          26                            52
  STAGE IIIC                          22                            31
  STAGE IV                            23                            38
  STAGE IVA                           13                            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 14(5Q22.2) MUTATED     4  30 130  20
  DEL PEAK 14(5Q22.2) WILD-TYPE  16  75 282  45
D41V5, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T1                           4                            16
  T2                          30                            75
  T3                         130                           282
  T4                          20                            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 14(5Q22.2) MUTATED    88  53  43
  DEL PEAK 14(5Q22.2) WILD-TYPE 253  95  69
D41V6, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          88                           253
  N1                          53                            95
  N2                          43                            69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 14(5Q22.2) MUTATED   123  27   7   1  22
  DEL PEAK 14(5Q22.2) WILD-TYPE 323  47   3   1  41
D41V7, multiclass
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  M0                          123                           323
  M1                           27                            47
  M1A                           7                             3
  M1B                           1                             1
  MX                           22                            41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    81 103
  DEL PEAK 14(5Q22.2) WILD-TYPE 202 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     81  103
  DEL PEAK 14(5Q22.2) WILD-TYPE  202  218
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          81                           202
  MALE                           103                           218
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                    113
  DEL PEAK 14(5Q22.2) WILD-TYPE                  265
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                              12
  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
D41V9, multiclass
                                clus
vv                               DEL PEAK 14(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                   113
  COLON MUCINOUS ADENOCARCINOMA                           12
  RECTAL ADENOCARCINOMA                                   56
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  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"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED     8 176
  DEL PEAK 14(5Q22.2) WILD-TYPE   1 419
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      8  176
  DEL PEAK 14(5Q22.2) WILD-TYPE    1  419
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                            8                             1
  YES                         176                           419
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q22.2) MUTATED   120   2  15   8
  DEL PEAK 14(5Q22.2) WILD-TYPE 316   3  21  21
D41V11, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                         120                           316
  R1                           2                             3
  R2                          15                            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"
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                          16    93
  DEL PEAK 14(5Q22.2) WILD-TYPE                        40   199
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK 14(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 15(6P25.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    54  17
  DEL PEAK 15(6P25.3) WILD-TYPE 412  92
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           71                           504 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           17                            92 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       37.02        15.52        16.04        25.18        24.16        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
       36.00         0.99        38.99        36.95        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 
       29.98        18.05        12.99        24.00         2.01        13.94 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O 
       30.02        18.05        27.02        38.07        26.01         0.92 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
        0.72         1.58         0.76         0.43         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
        2.24         3.06         2.14        29.06        22.98        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       11.01        14.99        20.19        17.75        17.85         7.53 
TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6317 TCGA-AF-2690 
       13.32        26.47       117.07        33.67        36.00        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3584 TCGA-AG-3593 
       13.55        19.10        12.72        14.50        24.00        34.03 
TCGA-AG-3598 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A011 TCGA-BM-6198 TCGA-DC-4745 
       50.04        36.03        13.94        37.02        10.19        10.98 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
       13.05         5.29        24.13        15.85        11.51 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        24.03        27.02        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       19.00        34.03        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         1.02         0.10 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        5.23        11.74         1.94         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.03        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
       14.04        81.37       119.93        35.97        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 
       14.76        30.28        67.00        24.13        17.95        43.04 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        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-3586 TCGA-AG-3587 
        8.02         7.07         1.02         2.01         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       117.07                        140.38 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                        17.23                         17.95 
[1] "0.4 - 117.1 (17.2)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.6"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    54  21
  DEL PEAK 15(6P25.3) WILD-TYPE 384 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     54   21
  DEL PEAK 15(6P25.3) WILD-TYPE  384  141
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  COLON                           54                           384
  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        28         1
  DEL PEAK 15(6P25.3) WILD-TYPE      93        1       29       143         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         20         72
                               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         46       54        22         2
D42V4, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              9                            93
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           28                           143
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            4                            22
  STAGE IIIA                           1                            20
  STAGE IIIB                           6                            72
  STAGE IIIC                           7                            46
  STAGE IV                             7                            54
  STAGE IVA                            5                            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 15(6P25.3) MUTATED     2   9  57  10
  DEL PEAK 15(6P25.3) WILD-TYPE  18  96 355  55
D42V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           2                            18
  T2                           9                            96
  T3                          57                           355
  T4                          10                            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 15(6P25.3) MUTATED    48  15  15
  DEL PEAK 15(6P25.3) WILD-TYPE 293 133  97
D42V6, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          48                           293
  N1                          15                           133
  N2                          15                            97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 15(6P25.3) MUTATED    55   8   3   0  10
  DEL PEAK 15(6P25.3) WILD-TYPE 391  66   7   2  53
D42V7, multiclass
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  M0                           55                           391
  M1                            8                            66
  M1A                           3                             7
  M1B                           0                             2
  MX                           10                            53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    29  49
  DEL PEAK 15(6P25.3) WILD-TYPE 254 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     29   49
  DEL PEAK 15(6P25.3) WILD-TYPE  254  272
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          29                           254
  MALE                            49                           272
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                     49
  DEL PEAK 15(6P25.3) WILD-TYPE                  329
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                               5
  DEL PEAK 15(6P25.3) WILD-TYPE                            54
                               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
D42V9, multiclass
                                clus
vv                               DEL PEAK 15(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                    49
  COLON MUCINOUS ADENOCARCINOMA                            5
  RECTAL ADENOCARCINOMA                                   18
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 15(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     329
  COLON MUCINOUS ADENOCARCINOMA                             54
  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"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     2  76
  DEL PEAK 15(6P25.3) WILD-TYPE   7 519
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      2   76
  DEL PEAK 15(6P25.3) WILD-TYPE    7  519
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                            2                             7
  YES                          76                           519
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6P25.3) MUTATED    55   0   3   6
  DEL PEAK 15(6P25.3) WILD-TYPE 381   5  33  23
D42V11, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          55                           381
  R1                           0                             5
  R2                           3                            33
  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                           1    38
  DEL PEAK 15(6P25.3) WILD-TYPE                        55   254
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 15(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     38
                                  clus
vv                                 DEL PEAK 15(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   55
  WHITE                                                      254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 16(6Q26) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED    63  22
  DEL PEAK 16(6Q26) WILD-TYPE 403  87
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         85                         490 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         22                          87 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6649 
       37.02        42.28        45.60        32.45        22.52        24.16 
TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       20.28         5.03        13.02        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3837 
       11.01        37.05        36.00        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        36.03        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        2.01        18.05        17.03         0.99        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         1.58         0.43         0.46        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 
        0.20         6.87         5.13        49.41         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
        3.06         2.14        11.01        13.05        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 
       14.99        20.19        17.75        15.12         7.53        13.32 
TCGA-DM-A1HA TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2690 
      131.51         1.55        33.67        82.39         5.98        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AG-3575 
       43.04        13.55        19.10        12.72        37.74        12.00 
TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 
       32.02        24.00        46.03        34.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 
       19.99        14.04         1.02        13.94        37.02         0.49 
TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 TCGA-G5-6233 
        0.72         9.37        13.05         5.29         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 16(6Q26) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
        5.98        19.00         5.03        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         5.52        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        11.74         1.94         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       12.99        13.02        15.02        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         1.32         7.92        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       52.80         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 
       14.76        30.28        67.00        24.13        17.95        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50         8.45        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         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        2.01         1.02        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-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-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        36.03        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        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         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-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        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.46        55.76        47.08 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     131.51                      140.38 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                      14.99                       18.05 
[1] "0.2 - 131.5 (15.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.8"
D43V2, continuous
D43V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    61  28
  DEL PEAK 16(6Q26) WILD-TYPE 377 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     61   28
  DEL PEAK 16(6Q26) WILD-TYPE  377  134
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  COLON                         61                         377
  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      89        1       28       151         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         20         68
                             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         39       49        23         1
D43V4, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                           13                          89
  STAGE IA                           0                           1
  STAGE II                           8                          28
  STAGE IIA                         20                         151
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          4                          22
  STAGE IIIA                         1                          20
  STAGE IIIB                        10                          68
  STAGE IIIC                        14                          39
  STAGE IV                          12                          49
  STAGE IVA                          4                          23
  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  95 348  53
D43V5, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T1                         5                          15
  T2                        10                          95
  T3                        64                         348
  T4                        12                          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 16(6Q26) MUTATED    43  18  29
  DEL PEAK 16(6Q26) WILD-TYPE 298 130  83
D43V6, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                        43                         298
  N1                        18                         130
  N2                        29                          83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 16(6Q26) MUTATED    59  15   2   1  13
  DEL PEAK 16(6Q26) WILD-TYPE 387  59   8   1  50
D43V7, multiclass
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  M0                         59                         387
  M1                         15                          59
  M1A                         2                           8
  M1B                         1                           1
  MX                         13                          50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    37  54
  DEL PEAK 16(6Q26) WILD-TYPE 246 267
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     37   54
  DEL PEAK 16(6Q26) WILD-TYPE  246  267
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        37                         246
  MALE                          54                         267
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                     53
  DEL PEAK 16(6Q26) WILD-TYPE                  325
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                               8
  DEL PEAK 16(6Q26) WILD-TYPE                            51
                             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
D43V9, multiclass
                                clus
vv                               DEL PEAK 16(6Q26) MUTATED
  COLON ADENOCARCINOMA                                  53
  COLON MUCINOUS ADENOCARCINOMA                          8
  RECTAL ADENOCARCINOMA                                 22
  RECTAL MUCINOUS ADENOCARCINOMA                         6
                                clus
vv                               DEL PEAK 16(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                   325
  COLON MUCINOUS ADENOCARCINOMA                           51
  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"
D43V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     2  89
  DEL PEAK 16(6Q26) WILD-TYPE   7 506
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      2   89
  DEL PEAK 16(6Q26) WILD-TYPE    7  506
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                          2                           7
  YES                        89                         506
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 16(6Q26) MUTATED    61   1   8   7
  DEL PEAK 16(6Q26) WILD-TYPE 375   4  28  22
D43V11, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                        61                         375
  R1                         1                           4
  R2                         8                          28
  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                        51   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                                 51
  WHITE                                                    253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 17(7Q31.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q31.1) MUTATED    12   2
  DEL PEAK 17(7Q31.1) WILD-TYPE 454 107
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           14                           561 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            2                           107 
$`DEL PEAK 17(7Q31.1) MUTATED`
TCGA-A6-3807 TCGA-AA-A00L TCGA-AA-A01R TCGA-AD-6548 TCGA-AU-3779 TCGA-CM-5341 
       34.65        17.03        35.01        21.37        14.50        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6932 TCGA-DM-A0XD TCGA-AG-3600 
       22.03         5.03        15.02        11.38        24.43         6.05 
TCGA-AG-A008 TCGA-DC-6682 
       13.94        13.05 

$`DEL PEAK 17(7Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         1.58         1.02         0.10         0.76         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.43         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41         1.51        12.00        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       14.76        30.28        67.00        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50         8.45        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       65.98        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         5.03                          0.07 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        35.01                        140.38 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                       16.025                        17.850 
[1] "5.0 - 35.0 (16.0)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1"  
D44V2, continuous
D44V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    12   4
  DEL PEAK 17(7Q31.1) WILD-TYPE 426 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     12    4
  DEL PEAK 17(7Q31.1) WILD-TYPE  426  158
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON                           12                           426
  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      99        1       36       164        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         20         77
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(7Q31.1) MUTATED            2        0         1         0
  DEL PEAK 17(7Q31.1) WILD-TYPE         51       61        26         2
D44V4, multiclass
            clus
vv           DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  STAGE I                              3                            99
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                            7                           164
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            1                            25
  STAGE IIIA                           1                            20
  STAGE IIIB                           1                            77
  STAGE IIIC                           2                            51
  STAGE IV                             0                            61
  STAGE IVA                            1                            26
  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  12   0
  DEL PEAK 17(7Q31.1) WILD-TYPE  20 101 400  65
D44V5, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           101
  T3                          12                           400
  T4                           0                            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 17(7Q31.1) MUTATED    10   3   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 331 145 109
D44V6, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                          10                           331
  N1                           3                           145
  N2                           3                           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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 17(7Q31.1) MUTATED    15   0   1   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 431  74   9   2  63
D44V7, multiclass
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  M0                           15                           431
  M1                            0                            74
  M1A                           1                             9
  M1B                           0                             2
  MX                            0                            63
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     9   7
  DEL PEAK 17(7Q31.1) WILD-TYPE 274 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      9    7
  DEL PEAK 17(7Q31.1) WILD-TYPE  274  314
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           9                           274
  MALE                             7                           314
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                     11
  DEL PEAK 17(7Q31.1) WILD-TYPE                  367
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                               1
  DEL PEAK 17(7Q31.1) WILD-TYPE                            58
                               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
D44V9, multiclass
                                clus
vv                               DEL PEAK 17(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    11
  COLON MUCINOUS ADENOCARCINOMA                            1
  RECTAL ADENOCARCINOMA                                    3
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     367
  COLON MUCINOUS ADENOCARCINOMA                             58
  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"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     0  16
  DEL PEAK 17(7Q31.1) WILD-TYPE   9 579
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      0   16
  DEL PEAK 17(7Q31.1) WILD-TYPE    9  579
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  NO                            0                             9
  YES                          16                           579
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q31.1) MUTATED    15   0   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 421   5  36  29
D44V11, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  R0                          15                           421
  R1                           0                             5
  R2                           0                            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"
D44V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q31.1) MUTATED                                  0     0
  DEL PEAK 17(7Q31.1) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(7Q31.1) MUTATED                           0    10
  DEL PEAK 17(7Q31.1) WILD-TYPE                        56   282
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 17(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     10
                                  clus
vv                                 DEL PEAK 17(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   56
  WHITE                                                      282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 18(8P23.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED   219  54
  DEL PEAK 18(8P23.2) WILD-TYPE 247  55
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          273                           302 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           54                            55 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       31.63        29.19        23.61        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       61.84        52.44         9.63         5.03         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
        1.02        38.99        24.03        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        19.99        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 
       19.00        36.00        85.05        37.02        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       29.98         2.01         2.01        34.03        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       17.03        15.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
       37.02         2.96        39.98         5.03        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 
        4.21         1.58         1.02         0.20        16.31        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 
        0.20         5.52         6.87        75.25         5.65        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       65.00        62.79        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 
        3.19         1.94         3.29         0.07         1.35        15.62 
TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       48.20        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 
       16.01         5.03        17.03        14.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 
       15.02        13.05        11.08        10.06        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        17.75         1.32         7.92        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G 
      140.38       131.51         6.12        26.47        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 
      117.07        13.38        13.64         1.55        16.31         0.53 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 
        8.35        23.51        74.56        61.87        44.68        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 
       35.93        36.72        36.00        26.43        35.80        91.79 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 
       10.98        10.52         5.98         5.59         5.49         6.64 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       12.72        37.74        10.39        15.39        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       65.98        32.02         1.02        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
       34.03         2.01         6.05         0.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98        32.98         0.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         1.02        17.03        20.98        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        51.98         1.94        38.96        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.45         0.72        10.19         4.73        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       10.98        11.01        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 
       57.24       129.27         0.49         2.40        15.85        16.34 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       31.30        14.86         0.39         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 
        5.06         5.26        46.65        23.38        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 
       37.25        16.04        14.53        32.45        30.44        33.53 
TCGA-A6-5664 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 
        1.02         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-3554 TCGA-AA-3555 
        8.05        19.07        19.07        29.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       20.98        13.94        61.02         6.97        54.02         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       50.04        47.05        11.01         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
        0.99        32.05        53.00        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3966 
       24.00        33.01        26.01        24.00        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       21.99        50.99        13.05        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        2.01         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       21.37        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.43         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       21.44        17.82         5.19        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        22.36        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 
      100.01         2.24         3.06         2.14         3.25         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-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-6172 
       29.03        16.04        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       12.95        11.08        11.01        12.03        14.99        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        17.85         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 
      119.93        98.24        95.18         8.61        11.11        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        29.59        16.24        33.67         1.28 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 
       35.41        19.43       107.67        28.21        82.39        43.07 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6322 
       53.62        55.04        51.75        45.11        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         1.32         5.19        26.99        17.29        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N 
       67.00        24.13        14.50         8.45        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         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 
       12.03        15.95        19.99         1.02         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A008 
       36.95        13.02        14.01        48.03         0.99        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
        6.02        37.02        36.03        49.97        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.49         0.69         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
        6.97         9.37         7.99        15.02        12.00        30.05 
TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.95        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        18.28        17.69        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46        37.51         1.02         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        17.03                         18.05 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.1"
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   184  98
  DEL PEAK 18(8P23.2) WILD-TYPE 254  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    184   98
  DEL PEAK 18(8P23.2) WILD-TYPE  254   64
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  COLON                          184                           254
  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        39        0       12        64         3
  DEL PEAK 18(8P23.2) WILD-TYPE      63        1       24       107         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(8P23.2) MUTATED           2        14         11         42
  DEL PEAK 18(8P23.2) WILD-TYPE         1        12         10         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(8P23.2) MUTATED           33       44        14         1
  DEL PEAK 18(8P23.2) WILD-TYPE         20       17        13         1
D45V4, multiclass
            clus
vv           DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                             39                            63
  STAGE IA                             0                             1
  STAGE II                            12                            24
  STAGE IIA                           64                           107
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           14                            12
  STAGE IIIA                          11                            10
  STAGE IIIB                          42                            36
  STAGE IIIC                          33                            20
  STAGE IV                            44                            17
  STAGE IVA                           14                            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 18(8P23.2) MUTATED     4  47 201  32
  DEL PEAK 18(8P23.2) WILD-TYPE  16  58 211  33
D45V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T1                           4                            16
  T2                          47                            58
  T3                         201                           211
  T4                          32                            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   131  79  72
  DEL PEAK 18(8P23.2) WILD-TYPE 210  69  40
D45V6, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                         131                           210
  N1                          79                            69
  N2                          72                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 18(8P23.2) MUTATED   196  50   6   1  28
  DEL PEAK 18(8P23.2) WILD-TYPE 250  24   4   1  35
D45V7, multiclass
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  M0                          196                           250
  M1                           50                            24
  M1A                           6                             4
  M1B                           1                             1
  MX                           28                            35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   120 164
  DEL PEAK 18(8P23.2) WILD-TYPE 163 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    120  164
  DEL PEAK 18(8P23.2) WILD-TYPE  163  157
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                         120                           163
  MALE                           164                           157
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                    167
  DEL PEAK 18(8P23.2) WILD-TYPE                  211
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                              16
  DEL PEAK 18(8P23.2) WILD-TYPE                            43
                               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
D45V9, multiclass
                                clus
vv                               DEL PEAK 18(8P23.2) MUTATED
  COLON ADENOCARCINOMA                                   167
  COLON MUCINOUS ADENOCARCINOMA                           16
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 18(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     211
  COLON MUCINOUS ADENOCARCINOMA                             43
  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"
D45V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     7 277
  DEL PEAK 18(8P23.2) WILD-TYPE   2 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      7  277
  DEL PEAK 18(8P23.2) WILD-TYPE    2  318
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                            7                             2
  YES                         277                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED   197   2  25   9
  DEL PEAK 18(8P23.2) WILD-TYPE 239   3  11  20
D45V11, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                         197                           239
  R1                           2                             3
  R2                          25                            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                          28   136
  DEL PEAK 18(8P23.2) WILD-TYPE                        28   156
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 19(8P22) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(8P22) MUTATED   221  62
  DEL PEAK 19(8P22) WILD-TYPE 245  47
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        283                         292 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                         62                          47 
$`DEL PEAK 19(8P22) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 
       31.63        30.44        29.19        23.61        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       20.28        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 
       37.05         1.02        38.99        24.03        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        19.99        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        14.01        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 
        5.98        37.05        19.00        36.00        85.05        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.99        33.07        36.03        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3956 
       24.03        27.02        29.98         2.01         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       16.08        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G 
       19.00        34.03        17.03        17.03        15.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J 
       31.00         1.02        33.04        37.02         2.96         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       41.00        40.96         4.21         1.58         1.02         0.20 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
        0.46        16.31        15.75         0.20         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25         5.65        83.80        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 
        3.29         1.35       102.44        15.62        48.20        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        21.99        13.02        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       13.05        11.08        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        17.75         1.32         7.92        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F 
      140.38        44.32       131.51         6.12        26.47        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07         8.61        13.38        11.11        13.64 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
        1.55        16.31         1.28         0.53         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       74.56        61.87        44.68        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        35.80        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 
       10.98        10.52         5.98         5.59         5.49         6.64 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       12.72        37.74        10.39        15.39        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       65.98        32.02         1.02        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
       29.98        32.98         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        1.02        17.03        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-AH-6547 
       10.98        51.98         1.94        38.96        41.00         1.45 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
        0.72        10.19         4.73        13.97        60.03        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        12.99        13.97        15.02        36.00         7.10 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 
      129.27         0.49         2.40        15.85        16.34        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       10.78        13.64        11.97         8.45         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       14.86         0.39         0.69         0.76         0.46        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 19(8P22) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 
        5.06         5.26        46.65        23.38        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 
       37.25        16.04        14.53        32.45        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       22.06        32.71        22.52         8.38        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 
       24.39        20.12        19.66        16.24        24.92         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       19.07        19.07        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 
       20.98        13.94        61.02         6.97         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       47.05         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3856 
       38.99        36.95        14.93        17.03        32.05         0.99 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
        0.99        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       32.02        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O 
       26.01        39.06        51.98        39.98         2.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 
        0.79         0.72         0.10         0.76         0.43         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 
       50.37        58.39         1.41        32.94         5.13        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       49.41         6.77       100.01         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.25         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       40.34        70.16        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       26.04         8.02        29.06        15.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        29.03        16.04        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        11.08        11.01        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        17.85         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        12.59         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 
       98.24        95.18        13.45         6.18        35.87        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.24        33.67        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       82.39        43.07        53.62        55.04        51.75        45.11 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       22.09        13.78        26.17        47.15        52.80         4.11 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         1.32         5.19        26.99        17.29        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N 
       67.00        24.13        14.50         8.45        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         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3878 
       12.03        15.95        19.99        19.99         1.02         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 
       19.99        36.95        13.02        14.01        48.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N 
       20.98        13.94         6.02        36.03        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.04         0.49         0.69         4.60         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
        6.05         6.97         9.37         7.99        15.02        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       30.05        12.95        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       16.41         8.61        17.46        37.51         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12        55.76        47.08 

  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                     140.38                      139.17 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                     17.030                      18.015 
[1] "0.2 - 140.4 (17.0)" "0.1 - 139.2 (18.0)"
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   196  98
  DEL PEAK 19(8P22) WILD-TYPE 242  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    196   98
  DEL PEAK 19(8P22) WILD-TYPE  242   64
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  COLON                        196                         242
  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        38        0       13        66         3
  DEL PEAK 19(8P22) WILD-TYPE      64        1       23       105         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P22) MUTATED           2        14         13         44
  DEL PEAK 19(8P22) WILD-TYPE         1        12          8         34
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P22) MUTATED           36       44        17         1
  DEL PEAK 19(8P22) WILD-TYPE         17       17        10         1
D46V4, multiclass
            clus
vv           DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  STAGE I                           38                          64
  STAGE IA                           0                           1
  STAGE II                          13                          23
  STAGE IIA                         66                         105
  STAGE IIB                          3                           7
  STAGE IIC                          2                           1
  STAGE III                         14                          12
  STAGE IIIA                        13                           8
  STAGE IIIB                        44                          34
  STAGE IIIC                        36                          17
  STAGE IV                          44                          17
  STAGE IVA                         17                          10
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 19(8P22) MUTATED     4  46 211  35
  DEL PEAK 19(8P22) WILD-TYPE  16  59 201  30
D46V5, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  T1                         4                          16
  T2                        46                          59
  T3                       211                         201
  T4                        35                          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   134  82  78
  DEL PEAK 19(8P22) WILD-TYPE 207  66  34
D46V6, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  N0                       134                         207
  N1                        82                          66
  N2                        78                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 19(8P22) MUTATED   204  53   6   1  29
  DEL PEAK 19(8P22) WILD-TYPE 242  21   4   1  34
D46V7, multiclass
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  M0                        204                         242
  M1                         53                          21
  M1A                         6                           4
  M1B                         1                           1
  MX                         29                          34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   129 167
  DEL PEAK 19(8P22) WILD-TYPE 154 154
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    129  167
  DEL PEAK 19(8P22) WILD-TYPE  154  154
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  FEMALE                       129                         154
  MALE                         167                         154
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                    178
  DEL PEAK 19(8P22) WILD-TYPE                  200
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                              17
  DEL PEAK 19(8P22) WILD-TYPE                            42
                             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
D46V9, multiclass
                                clus
vv                               DEL PEAK 19(8P22) MUTATED
  COLON ADENOCARCINOMA                                 178
  COLON MUCINOUS ADENOCARCINOMA                         17
  RECTAL ADENOCARCINOMA                                 89
  RECTAL MUCINOUS ADENOCARCINOMA                         7
                                clus
vv                               DEL PEAK 19(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                   200
  COLON MUCINOUS ADENOCARCINOMA                           42
  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"
D46V10, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED     7 289
  DEL PEAK 19(8P22) WILD-TYPE   2 306
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED      7  289
  DEL PEAK 19(8P22) WILD-TYPE    2  306
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  NO                          7                           2
  YES                       289                         306
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(8P22) MUTATED   209   2  25   8
  DEL PEAK 19(8P22) WILD-TYPE 227   3  11  21
D46V11, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  R0                       209                         227
  R1                         2                           3
  R2                        25                          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                          28   147
  DEL PEAK 19(8P22) WILD-TYPE                        28   145
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 19(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               28
  WHITE                                                  147
                                  clus
vv                                 DEL PEAK 19(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 20(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 431  98
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           46                           529 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           11                            98 
$`DEL PEAK 20(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 
       17.79        42.28        44.91        15.52        36.53        20.61 
TCGA-A6-6654 TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-3681 
       23.87        38.99        34.03        14.01         2.01         5.98 
TCGA-AA-3842 TCGA-AA-3989 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02F TCGA-AY-6196 
       37.02         7.96         0.99        31.00        39.98         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 
        5.52         6.87        37.02        17.03        13.05        13.51 
TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6625 
       17.75        49.91       131.51         1.55        23.51        91.79 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3582 TCGA-AG-3728 TCGA-AG-3890 
       17.95        13.55        12.72         1.02        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-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       23.38        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
       15.75        21.44        17.82         5.19        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       20.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        20.42        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        10.52         2.79         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       30.28        67.00        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         8.45        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         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-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         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.99        12.00        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-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 
       37.51        31.30        14.86         1.02         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                        17.39                         17.95 
[1] "0.2 - 131.5 (17.4)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.3"
D47V2, continuous
D47V3, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    30  16
  DEL PEAK 20(8Q11.1) WILD-TYPE 408 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     30   16
  DEL PEAK 20(8Q11.1) WILD-TYPE  408  146
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  COLON                           30                           408
  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      98        1       36       158         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         19         71
                               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         46       55        23         1
D47V4, multiclass
            clus
vv           DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  STAGE I                              4                            98
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                           13                           158
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           2                            19
  STAGE IIIB                           7                            71
  STAGE IIIC                           7                            46
  STAGE IV                             6                            55
  STAGE IVA                            4                            23
  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  98 377  60
D47V5, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  T1                           0                            20
  T2                           7                            98
  T3                          35                           377
  T4                           5                            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 20(8Q11.1) MUTATED    19  16  12
  DEL PEAK 20(8Q11.1) WILD-TYPE 322 132 100
D47V6, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  N0                          19                           322
  N1                          16                           132
  N2                          12                           100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 20(8Q11.1) MUTATED    32   8   2   1   2
  DEL PEAK 20(8Q11.1) WILD-TYPE 414  66   8   1  61
D47V7, multiclass
     clus
vv    DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  M0                           32                           414
  M1                            8                            66
  M1A                           2                             8
  M1B                           1                             1
  MX                            2                            61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    18  29
  DEL PEAK 20(8Q11.1) WILD-TYPE 265 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     18   29
  DEL PEAK 20(8Q11.1) WILD-TYPE  265  292
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  FEMALE                          18                           265
  MALE                            29                           292
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                     26
  DEL PEAK 20(8Q11.1) WILD-TYPE                  352
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                               4
  DEL PEAK 20(8Q11.1) WILD-TYPE                            55
                               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
D47V9, 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                                     352
  COLON MUCINOUS ADENOCARCINOMA                             55
  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"
D47V10, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED     1  46
  DEL PEAK 20(8Q11.1) WILD-TYPE   8 549
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED      1   46
  DEL PEAK 20(8Q11.1) WILD-TYPE    8  549
     clus
vv    DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  NO                            1                             8
  YES                          46                           549
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(8Q11.1) MUTATED    38   0   4   0
  DEL PEAK 20(8Q11.1) WILD-TYPE 398   5  32  29
D47V11, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  R0                          38                           398
  R1                           0                             5
  R2                           4                            32
  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                        50   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                                   50
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 21(9P24.2) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(9P24.2) MUTATED    62  16
  DEL PEAK 21(9P24.2) WILD-TYPE 404  93
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           78                           497 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           16                            93 
$`DEL PEAK 21(9P24.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 
       37.02        43.43        36.53        14.53        29.16        24.16 
TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
       21.76        61.84         6.97        38.99         9.07        29.00 
TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3867 
       24.00        19.99        37.05        85.05        25.02        24.03 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3972 TCGA-AA-A004 TCGA-AA-A01F 
       12.99        24.00        20.98        50.99        13.94        32.02 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-6605 
       40.96         4.21         0.20        16.31         5.65         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5348 
        3.19         1.94         3.29         0.26         8.02        22.98 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       13.02        15.02        13.05        11.08        11.01        10.06 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 
       20.19         1.32         7.92         7.53        38.20        14.04 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2687 TCGA-AF-2692 
       33.67         8.35        82.39         5.98        24.13        13.55 
TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 
       65.98         2.01        34.03         6.05         1.02        19.99 
TCGA-AG-3896 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 
        1.02        15.95        12.00         1.94        38.96         0.49 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6160 
       10.19         6.05         4.73        13.97        11.01        30.05 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6814 
       57.24        24.13        51.48         0.49        16.31         0.53 

$`DEL PEAK 21(9P24.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        16.04        34.65        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        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-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-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
        2.01        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       11.51        20.42        17.75        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       47.15        52.80         4.11        10.98        10.52         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
        6.64        14.76        30.28        67.00        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        19.10        12.72        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
        8.45        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         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99         0.99         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-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        36.03         9.07         1.02        31.00        70.03 
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-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         1.45         0.69         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97         9.37        60.03         7.99        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       41.36       129.27        32.61         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-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.66         0.69         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                       14.285                        18.050 
[1] "0.2 - 85.0 (14.3)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    55  26
  DEL PEAK 21(9P24.2) WILD-TYPE 383 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     55   26
  DEL PEAK 21(9P24.2) WILD-TYPE  383  136
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  COLON                           55                           383
  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        18         1
  DEL PEAK 21(9P24.2) WILD-TYPE      89        1       32       153         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         18         66
                               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         44       49        23         1
D48V4, multiclass
            clus
vv           DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  STAGE I                             13                            89
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           18                           153
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            3                            23
  STAGE IIIA                           3                            18
  STAGE IIIB                          12                            66
  STAGE IIIC                           9                            44
  STAGE IV                            12                            49
  STAGE IVA                            4                            23
  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  17  51  12
  DEL PEAK 21(9P24.2) WILD-TYPE  18  88 361  53
D48V5, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  T1                           2                            18
  T2                          17                            88
  T3                          51                           361
  T4                          12                            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 21(9P24.2) MUTATED    38  23  20
  DEL PEAK 21(9P24.2) WILD-TYPE 303 125  92
D48V6, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  N0                          38                           303
  N1                          23                           125
  N2                          20                            92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 21(9P24.2) MUTATED    57  15   2   1   6
  DEL PEAK 21(9P24.2) WILD-TYPE 389  59   8   1  57
D48V7, multiclass
     clus
vv    DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  M0                           57                           389
  M1                           15                            59
  M1A                           2                             8
  M1B                           1                             1
  MX                            6                            57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    30  52
  DEL PEAK 21(9P24.2) WILD-TYPE 253 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     30   52
  DEL PEAK 21(9P24.2) WILD-TYPE  253  269
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  FEMALE                          30                           253
  MALE                            52                           269
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                     52
  DEL PEAK 21(9P24.2) WILD-TYPE                  326
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                               3
  DEL PEAK 21(9P24.2) WILD-TYPE                            56
                               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
D48V9, multiclass
                                clus
vv                               DEL PEAK 21(9P24.2) MUTATED
  COLON ADENOCARCINOMA                                    52
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   25
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 21(9P24.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     326
  COLON MUCINOUS ADENOCARCINOMA                             56
  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"
D48V10, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED     2  80
  DEL PEAK 21(9P24.2) WILD-TYPE   7 515
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED      2   80
  DEL PEAK 21(9P24.2) WILD-TYPE    7  515
     clus
vv    DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  NO                            2                             7
  YES                          80                           515
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(9P24.2) MUTATED    52   2   7   3
  DEL PEAK 21(9P24.2) WILD-TYPE 384   3  29  26
D48V11, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  R0                          52                           384
  R1                           2                             3
  R2                           7                            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"
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                           6    43
  DEL PEAK 21(9P24.2) WILD-TYPE                        50   249
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 21(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     43
                                  clus
vv                                 DEL PEAK 21(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   50
  WHITE                                                      249
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(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 374  91
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           110                            465 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            18                             91 
$`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        17.79        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3673 
        1.02         6.97        13.02        19.99        54.02        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       37.05        36.00        85.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       24.03         2.01        50.99        24.00         7.96        34.03 
TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       18.05        42.02        21.99         0.99        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4323 
        1.02         0.43         0.46        14.50         0.20         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 
        5.65         5.13        65.00        62.79        29.56         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       11.08        17.75        15.12         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 
       13.41        82.39        61.87        55.04        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 
       26.04        46.75         1.32        30.28        24.13        13.55 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 
       12.72        10.39        65.98        46.03        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         0.49         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        36.00        13.05        10.06 
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 
       14.86        26.43 

$`DEL PEAK 22(10P15.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        52.44         5.03         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       17.03        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       26.01        25.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.10         0.76         0.20         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 
        6.87        75.25        50.37        58.39        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02         8.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        18.25         1.32         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       19.43       107.67        28.21         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       43.07        53.62        44.68        51.75        45.11        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        14.76        67.00        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-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         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        32.02        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02        17.03         0.99        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         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       13.97        60.03         7.99        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00         7.10        30.05        12.95         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        37.51        31.30         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                        129.27                         140.38 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                         17.77                          17.85 
[1] "0.2 - 129.3 (17.8)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.2"
D49V2, continuous
D49V3, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    77  34
  DEL PEAK 22(10P15.3) WILD-TYPE 361 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     77   34
  DEL PEAK 22(10P15.3) WILD-TYPE  361  128
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  COLON                            77                            361
  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      83        1       30       150        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(10P15.3) MUTATED           1         2          7         15
  DEL PEAK 22(10P15.3) WILD-TYPE         2        24         14         63
                                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         40       44        20         1
D49V4, multiclass
            clus
vv           DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            21                            150
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            7                             14
  STAGE IIIB                           15                             63
  STAGE IIIC                           13                             40
  STAGE IV                             17                             44
  STAGE IVA                             7                             20
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 22(10P15.3) MUTATED     2  23  74  13
  DEL PEAK 22(10P15.3) WILD-TYPE  18  82 338  52
D49V5, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  T1                            2                             18
  T2                           23                             82
  T3                           74                            338
  T4                           13                             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 22(10P15.3) MUTATED    51  32  29
  DEL PEAK 22(10P15.3) WILD-TYPE 290 116  83
D49V6, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  N0                           51                            290
  N1                           32                            116
  N2                           29                             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 22(10P15.3) MUTATED    77  21   2   1  10
  DEL PEAK 22(10P15.3) WILD-TYPE 369  53   8   1  53
D49V7, multiclass
     clus
vv    DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  M0                            77                            369
  M1                            21                             53
  M1A                            2                              8
  M1B                            1                              1
  MX                            10                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    51  61
  DEL PEAK 22(10P15.3) WILD-TYPE 232 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     51   61
  DEL PEAK 22(10P15.3) WILD-TYPE  232  260
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  FEMALE                           51                            232
  MALE                             61                            260
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                     69
  DEL PEAK 22(10P15.3) WILD-TYPE                  309
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                               8
  DEL PEAK 22(10P15.3) WILD-TYPE                            51
                                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
D49V9, 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                                      309
  COLON MUCINOUS ADENOCARCINOMA                              51
  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"
D49V10, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED     5 107
  DEL PEAK 22(10P15.3) WILD-TYPE   4 488
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED      5  107
  DEL PEAK 22(10P15.3) WILD-TYPE    4  488
     clus
vv    DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  NO                             5                              4
  YES                          107                            488
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(10P15.3) MUTATED    83   0   6   6
  DEL PEAK 22(10P15.3) WILD-TYPE 353   5  30  23
D49V11, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  R0                           83                            353
  R1                            0                              5
  R2                            6                             30
  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                        47   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                                    47
  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"

Clustering(50) Variable = DEL PEAK 23(10Q21.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10Q21.1) MUTATED   105  25
  DEL PEAK 23(10Q21.1) WILD-TYPE 361  84
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           130                            445 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            25                             84 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4107 
       37.02        17.79        35.11        45.60        34.65        32.45 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 
       30.44        32.71        29.16        22.52        25.18        20.61 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       23.87        61.84        52.44         9.63         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       38.99        33.99        21.01        13.02        19.99         6.05 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 
       50.04        37.05        36.00        85.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3989 
       17.03        24.03         2.01        21.99        50.99         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X TCGA-AA-A02F 
       34.03        42.02         0.99         1.02        26.01        39.98 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 
        5.03        41.00         0.79         1.02         0.43        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
       16.31         0.20         6.87         5.65        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       29.56         3.19         2.24         3.29         0.26         1.35 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
        8.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 
       29.03        13.02        15.02        11.08        11.08        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 
        7.92        15.12        17.85         7.53         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 TCGA-G4-6307 
       12.00        11.38        35.97       117.07        11.11        55.04 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GC 
       35.93        36.72        26.04        91.79        46.75         1.32 
TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 
        5.19        30.28        24.13        13.55        12.72         8.45 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
       10.39        65.98        32.02         1.02         2.01        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
       34.03         6.05        29.98         1.02        36.95         1.02 
TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       19.99        13.94         6.02        25.97        23.01        12.00 
TCGA-AG-A026 TCGA-AG-A02X TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-6155 
        1.94        41.00         6.97         4.73        13.97        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 
       36.00        13.05        10.06       129.27        17.00        16.31 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       16.41        14.86         0.46        26.43 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       16.04        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 
       20.12        19.66        20.28        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.96         2.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.58         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41        32.94         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        1.94         3.06         2.14         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        16.01        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        20.42        18.25         1.32 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       26.47        81.37       119.93        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        51.75        45.11        39.42        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       14.50        15.39        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
       12.00         8.02         7.07        24.00         1.02         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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       19.99        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.98        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.05         9.37        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       12.95         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        18.28        15.85        17.69        16.34         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        129.27                         140.38 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        16.705                         18.050 
[1] "0.2 - 129.3 (16.7)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    94  40
  DEL PEAK 23(10Q21.1) WILD-TYPE 344 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     94   40
  DEL PEAK 23(10Q21.1) WILD-TYPE  344  122
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON                            94                            344
  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        31         1
  DEL PEAK 23(10Q21.1) WILD-TYPE      82        1       29       140         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10Q21.1) MUTATED           1         2          7         18
  DEL PEAK 23(10Q21.1) WILD-TYPE         2        24         14         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10Q21.1) MUTATED           19       19         6         1
  DEL PEAK 23(10Q21.1) WILD-TYPE         34       42        21         1
D50V4, multiclass
            clus
vv           DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  STAGE I                              20                             82
  STAGE IA                              0                              1
  STAGE II                              7                             29
  STAGE IIA                            31                            140
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            7                             14
  STAGE IIIB                           18                             60
  STAGE IIIC                           19                             34
  STAGE IV                             19                             42
  STAGE IVA                             6                             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 23(10Q21.1) MUTATED     3  24  94  14
  DEL PEAK 23(10Q21.1) WILD-TYPE  17  81 318  51
D50V5, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  T1                            3                             17
  T2                           24                             81
  T3                           94                            318
  T4                           14                             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 23(10Q21.1) MUTATED    66  36  33
  DEL PEAK 23(10Q21.1) WILD-TYPE 275 112  79
D50V6, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  N0                           66                            275
  N1                           36                            112
  N2                           33                             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 23(10Q21.1) MUTATED    97  22   2   1  12
  DEL PEAK 23(10Q21.1) WILD-TYPE 349  52   8   1  51
D50V7, multiclass
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  M0                            97                            349
  M1                            22                             52
  M1A                            2                              8
  M1B                            1                              1
  MX                            12                             51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    62  73
  DEL PEAK 23(10Q21.1) WILD-TYPE 221 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     62   73
  DEL PEAK 23(10Q21.1) WILD-TYPE  221  248
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  FEMALE                           62                            221
  MALE                             73                            248
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                     87
  DEL PEAK 23(10Q21.1) WILD-TYPE                  291
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                               7
  DEL PEAK 23(10Q21.1) WILD-TYPE                            52
                                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
D50V9, multiclass
                                clus
vv                               DEL PEAK 23(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                     87
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      291
  COLON MUCINOUS ADENOCARCINOMA                              52
  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"
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED     5 130
  DEL PEAK 23(10Q21.1) WILD-TYPE   4 465
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED      5  130
  DEL PEAK 23(10Q21.1) WILD-TYPE    4  465
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                             5                              4
  YES                          130                            465
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10Q21.1) MUTATED    95   2  12   7
  DEL PEAK 23(10Q21.1) WILD-TYPE 341   3  24  22
D50V11, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           95                            341
  R1                            2                              3
  R2                           12                             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"
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                          14    65
  DEL PEAK 23(10Q21.1) WILD-TYPE                        42   227
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 23(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      65
                                  clus
vv                                 DEL PEAK 23(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    42
  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"

Clustering(51) Variable = DEL PEAK 24(10Q23.31) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED   125  24
  DEL PEAK 24(10Q23.31) WILD-TYPE 341  85
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            149                             426 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             24                              85 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        17.79        42.28        35.11        45.60        13.94 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       24.16        23.87        61.84         9.63         1.02         6.97 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 
        9.07        19.07        33.99        13.02        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 
        6.05        54.02        50.04        11.01        37.05        36.00 
TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       85.05        36.95        33.07        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       24.03         2.01        50.99         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 
        0.99        33.04        26.01        39.98        41.00         1.02 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
        0.43         0.46        14.50        16.31         5.19         5.52 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
        5.65        65.00        62.79        29.56         3.19         2.24 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       30.08         5.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 
       15.02        13.05        11.08        11.08        10.06        19.59 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       17.75        18.25         7.92        17.85        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.13         9.04        13.41       130.65        13.32       140.38 
TCGA-DM-A285 TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 
        6.12        11.11        16.24        33.67        55.04        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-NH-A8F7 
       36.00        26.04        13.78        46.75         1.32         5.19 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       30.28        24.13        17.95        13.55        12.72        10.39 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       65.98        32.02         1.02        46.03        34.03        50.04 
TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 
        6.05        29.98         1.02        36.95         1.02        19.99 
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 
        4.60        10.19         6.97         4.73        13.97        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
       36.00        13.05        10.06       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 
       14.86         0.66         0.46        47.08        26.43 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       19.66        20.28        16.24        24.92        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
       63.98         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03         8.05        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.05        47.01        15.02         5.98        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        37.02        39.06        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        1.58         0.10         0.76         0.20         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A8YK 
        0.95        15.75         0.20        21.44        17.82         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
      100.01         5.23        11.74         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02         8.02        26.04        27.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       16.01        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        11.01        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19        20.42         1.32        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        51.75        45.11        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.43        22.09        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.59         5.49        26.99        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       67.00        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       14.50         8.45        15.39        20.02        86.63        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         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       24.00         2.01        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        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         0.99        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 
        0.49         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 
        6.05         9.37        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       12.95         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        37.51        31.30         0.39         1.02 
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 
                           0.26                            0.07 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          17.00                           18.05 
[1] "0.3 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.2"
D51V2, continuous
D51V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   105  51
  DEL PEAK 24(10Q23.31) WILD-TYPE 333 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    105   51
  DEL PEAK 24(10Q23.31) WILD-TYPE  333  111
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON                            105                             333
  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        40         2
  DEL PEAK 24(10Q23.31) WILD-TYPE      81        0       30       131         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q23.31) MUTATED           1         6         10         20
  DEL PEAK 24(10Q23.31) WILD-TYPE         2        20         11         58
                                 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         36       39        21         0
D51V4, multiclass
            clus
vv           DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  STAGE I                               21                              81
  STAGE IA                               1                               0
  STAGE II                               6                              30
  STAGE IIA                             40                             131
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              6                              20
  STAGE IIIA                            10                              11
  STAGE IIIB                            20                              58
  STAGE IIIC                            17                              36
  STAGE IV                              22                              39
  STAGE IVA                              6                              21
  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  24 112  16
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  81 300  49
D51V5, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  T1                             3                              17
  T2                            24                              81
  T3                           112                             300
  T4                            16                              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 24(10Q23.31) MUTATED    76  44  36
  DEL PEAK 24(10Q23.31) WILD-TYPE 265 104  76
D51V6, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  N0                            76                             265
  N1                            44                             104
  N2                            36                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 24(10Q23.31) MUTATED   114  25   2   2  12
  DEL PEAK 24(10Q23.31) WILD-TYPE 332  49   8   0  51
D51V7, multiclass
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  M0                            114                             332
  M1                             25                              49
  M1A                             2                               8
  M1B                             2                               0
  MX                             12                              51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    74  83
  DEL PEAK 24(10Q23.31) WILD-TYPE 209 238
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     74   83
  DEL PEAK 24(10Q23.31) WILD-TYPE  209  238
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                            74                             209
  MALE                              83                             238
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                     96
  DEL PEAK 24(10Q23.31) WILD-TYPE                  282
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                               8
  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
D51V9, multiclass
                                clus
vv                               DEL PEAK 24(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                      96
  COLON MUCINOUS ADENOCARCINOMA                              8
  RECTAL ADENOCARCINOMA                                     42
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       282
  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"
D51V10, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED     6 151
  DEL PEAK 24(10Q23.31) WILD-TYPE   3 444
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED      6  151
  DEL PEAK 24(10Q23.31) WILD-TYPE    3  444
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                              6                               3
  YES                           151                             444
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(10Q23.31) MUTATED   115   1  12   6
  DEL PEAK 24(10Q23.31) WILD-TYPE 321   4  24  23
D51V11, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                           115                             321
  R1                             1                               4
  R2                            12                              24
  RX                             6                              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          15    81
  DEL PEAK 24(10Q23.31) WILD-TYPE                        41   211
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   15
  WHITE                                                       81
                                  clus
vv                                 DEL PEAK 24(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     41
  WHITE                                                        211
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 25(10Q25.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q25.2) MUTATED   115  31
  DEL PEAK 25(10Q25.2) WILD-TYPE 351  78
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           146                            429 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                            31                             78 
$`DEL PEAK 25(10Q25.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
        5.06        37.02        17.79        42.28        35.11        45.60 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.61        23.87        61.84        52.44         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3548 
        1.02         6.97         9.07        37.05        29.00        33.99 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3680 
       13.02        19.99         6.05         2.01        50.04        11.01 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3818 
       37.05        36.00         5.03        85.05         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 
       36.95        33.07         0.99        17.03        24.03         2.01 
TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       50.99         7.96        34.03        42.02         0.99        33.04 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
       26.01        39.06         0.92        41.00         1.02         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 
        0.43        14.50        16.31         5.52         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       62.79        29.56         3.19         3.29         0.26         1.35 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        2.01         8.02         8.02        29.06        22.03         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       11.08        10.06        17.75         7.92        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       10.13         9.04        13.41        13.32       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 
        6.12        35.97        11.11        16.24        33.67        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GC 
       36.72        36.00        26.04        91.79        46.75         1.32 
TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 
        5.19        30.28        24.13        17.95        13.55        12.72 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 
       10.39        65.98        32.02        34.03         6.05        29.98 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A008 
       36.95        17.03         1.02        19.99        36.03        13.94 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A02X 
       25.97        37.02        12.00        70.03        10.98        41.00 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        4.60        10.19         4.73        13.97        36.00        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 
       13.05        10.06       129.27        24.13         2.40        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 
       16.31        16.41        11.97        14.86         0.66         0.46 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK 25(10Q25.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        5.26        46.65        43.76        43.43        23.38        44.91 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       19.66        20.28        16.24        24.92         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02         5.98        19.00        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       35.01         1.02        35.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.58         0.10         0.76         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       48.20        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.42        18.25         1.32        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
        6.18        35.87         1.55        16.31        29.59         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       44.68        51.75        45.11        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 
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-A56K TCGA-AF-A56N TCGA-AG-3574 
        8.45        15.39        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 
       32.98         0.99         0.99        19.99         1.02        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       35.01        14.01        48.03        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03         0.99        20.98         6.02        23.01 
TCGA-AG-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-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 
        0.49         1.45         0.69         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        7.10        12.95         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-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-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39         1.02         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.76        18.28        55.76 

  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        17.015                         18.050 
[1] "0.2 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.2"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   106  47
  DEL PEAK 25(10Q25.2) WILD-TYPE 332 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    106   47
  DEL PEAK 25(10Q25.2) WILD-TYPE  332  115
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON                           106                            332
  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        41         0
  DEL PEAK 25(10Q25.2) WILD-TYPE      83        1       28       130        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q25.2) MUTATED           1         7          7         19
  DEL PEAK 25(10Q25.2) WILD-TYPE         2        19         14         59
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q25.2) MUTATED           19       22         6         1
  DEL PEAK 25(10Q25.2) WILD-TYPE         34       39        21         1
D52V4, multiclass
            clus
vv           DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            41                            130
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                            7                             14
  STAGE IIIB                           19                             59
  STAGE IIIC                           19                             34
  STAGE IV                             22                             39
  STAGE IVA                             6                             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 25(10Q25.2) MUTATED     3  22 114  14
  DEL PEAK 25(10Q25.2) WILD-TYPE  17  83 298  51
D52V5, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  T1                            3                             17
  T2                           22                             83
  T3                          114                            298
  T4                           14                             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 25(10Q25.2) MUTATED    73  42  38
  DEL PEAK 25(10Q25.2) WILD-TYPE 268 106  74
D52V6, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  N0                           73                            268
  N1                           42                            106
  N2                           38                             74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 25(10Q25.2) MUTATED   112  24   3   1  12
  DEL PEAK 25(10Q25.2) WILD-TYPE 334  50   7   1  51
D52V7, multiclass
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  M0                           112                            334
  M1                            24                             50
  M1A                            3                              7
  M1B                            1                              1
  MX                            12                             51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    73  81
  DEL PEAK 25(10Q25.2) WILD-TYPE 210 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     73   81
  DEL PEAK 25(10Q25.2) WILD-TYPE  210  240
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  FEMALE                           73                            210
  MALE                             81                            240
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                     97
  DEL PEAK 25(10Q25.2) WILD-TYPE                  281
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                               9
  DEL PEAK 25(10Q25.2) WILD-TYPE                            50
                                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
D52V9, 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                                      281
  COLON MUCINOUS ADENOCARCINOMA                              50
  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"
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED     6 148
  DEL PEAK 25(10Q25.2) WILD-TYPE   3 447
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED      6  148
  DEL PEAK 25(10Q25.2) WILD-TYPE    3  447
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  NO                             6                              3
  YES                          148                            447
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(10Q25.2) MUTATED   112   1  12   6
  DEL PEAK 25(10Q25.2) WILD-TYPE 324   4  24  23
D52V11, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  R0                          112                            324
  R1                            1                              4
  R2                           12                             24
  RX                            6                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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                          15    77
  DEL PEAK 25(10Q25.2) WILD-TYPE                        41   215
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      77
                                  clus
vv                                 DEL PEAK 25(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 26(11Q22.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11Q22.3) MUTATED    83  20
  DEL PEAK 26(11Q22.3) WILD-TYPE 383  89
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           103                            472 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                            20                             89 
$`DEL PEAK 26(11Q22.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       37.02        45.60        15.52        36.53        32.45        30.44 
TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3511 
       22.52        24.16        21.76        23.87         5.03         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3558 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3680 
        9.07        37.05        20.98         6.05         2.01        11.01 
TCGA-AA-3692 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.00        32.05        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-A00F 
        2.01        34.03         2.01        21.99        50.99        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J 
       42.02        32.02        33.04         2.96        39.98        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 
        1.58         1.02         0.43        14.50         0.95         0.20 
TCGA-AY-A69D TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 
        5.52         1.41         2.14         0.26         2.01        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        14.04        11.01        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1D6 
       14.99        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        36.72        36.00        46.75         4.11 
TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
        1.32        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-3593 
       15.39        10.39        32.02         7.07        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 
        2.01         6.05         0.99        32.98         1.02        13.94 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 
       12.00        70.03        64.01        10.98        41.00         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 
        0.69         0.72        10.19        13.97        13.97         7.10 
TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6881 
       30.05         5.29        24.13        20.91        17.00        16.41 
TCGA-EI-7004 
        8.45 

$`DEL PEAK 26(11Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
       17.79        42.28        44.91        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        34.65        14.53        32.91        31.63 
TCGA-A6-5660 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-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        52.44         9.63         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
       63.98         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       19.99        13.94        19.99        61.02        78.08         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-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       20.98        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02         0.99        12.00        31.00 
TCGA-AA-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-AD-5900 
        0.92        22.03        41.00        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       15.75        21.44        17.82         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.98        16.01        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20        92.75        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        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 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       45.11        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       10.98        10.52         2.79         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
        8.45        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         1.02         2.01        24.00         1.02 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.04         1.45         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37         4.73        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       19.96        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                        130.65                         140.38 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                         15.02                          18.05 
[1] "0.2 - 130.7 (15.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    69  36
  DEL PEAK 26(11Q22.3) WILD-TYPE 369 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     69   36
  DEL PEAK 26(11Q22.3) WILD-TYPE  369  126
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON                            69                            369
  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        21        0        4        26         0
  DEL PEAK 26(11Q22.3) WILD-TYPE      81        1       32       145        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         18         63
                                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         42       47        22         1
D53V4, multiclass
            clus
vv           DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  STAGE I                              21                             81
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            26                            145
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                            3                             18
  STAGE IIIB                           15                             63
  STAGE IIIC                           11                             42
  STAGE IV                             14                             47
  STAGE IVA                             5                             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 26(11Q22.3) MUTATED     4  18  72  15
  DEL PEAK 26(11Q22.3) WILD-TYPE  16  87 340  50
D53V5, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  T1                            4                             16
  T2                           18                             87
  T3                           72                            340
  T4                           15                             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 26(11Q22.3) MUTATED    53  32  23
  DEL PEAK 26(11Q22.3) WILD-TYPE 288 116  89
D53V6, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  N0                           53                            288
  N1                           32                            116
  N2                           23                             89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 26(11Q22.3) MUTATED    75  14   3   1  13
  DEL PEAK 26(11Q22.3) WILD-TYPE 371  60   7   1  50
D53V7, multiclass
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  M0                            75                            371
  M1                            14                             60
  M1A                            3                              7
  M1B                            1                              1
  MX                            13                             50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    53  56
  DEL PEAK 26(11Q22.3) WILD-TYPE 230 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     53   56
  DEL PEAK 26(11Q22.3) WILD-TYPE  230  265
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  FEMALE                           53                            230
  MALE                             56                            265
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                     61
  DEL PEAK 26(11Q22.3) WILD-TYPE                  317
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                               8
  DEL PEAK 26(11Q22.3) WILD-TYPE                            51
                                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
D53V9, multiclass
                                clus
vv                               DEL PEAK 26(11Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     61
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      317
  COLON MUCINOUS ADENOCARCINOMA                              51
  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"
D53V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED     3 106
  DEL PEAK 26(11Q22.3) WILD-TYPE   6 489
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED      3  106
  DEL PEAK 26(11Q22.3) WILD-TYPE    6  489
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  NO                             3                              6
  YES                          106                            489
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(11Q22.3) MUTATED    77   0   9   4
  DEL PEAK 26(11Q22.3) WILD-TYPE 359   5  27  25
D53V11, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  R0                           77                            359
  R1                            0                              5
  R2                            9                             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"
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                           5    53
  DEL PEAK 26(11Q22.3) WILD-TYPE                        51   239
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 26(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    51
  WHITE                                                       239
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 27(12P13.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.1) MUTATED    63  22
  DEL PEAK 27(12P13.1) WILD-TYPE 403  87
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            85                            490 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            22                             87 
$`DEL PEAK 27(12P13.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
       37.02        17.79        45.60        34.65        36.53        30.44 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3544 
       24.69        20.28        61.84         9.63        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3688 
       33.99        13.02        78.08         2.01        50.04        19.00 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A01F 
       31.07        17.03        24.03         2.01        50.99        32.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AZ-4684 
       33.04         2.96         1.58         1.02         0.43        65.00 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        2.14         0.07        48.20         8.02         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 
       29.03        15.02        11.01        11.08        10.06         1.32 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-F4-6460 
       15.12         7.53        11.38        13.32        12.59        13.38 
TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 
       11.11        16.24        61.87        36.72        36.00        35.80 
TCGA-NH-A50U TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       10.98         5.19        30.28        43.04        13.55        19.10 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3593 
       10.39        14.50        15.39        20.02        36.03        34.03 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3898 TCGA-AG-A00C TCGA-AG-A01W TCGA-AG-A026 
       29.98         1.02        48.03         6.02        70.03         1.94 
TCGA-AH-6544 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG 
        0.49         6.05        13.97         7.10        24.13        51.48 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       20.91        17.00        16.31        16.41        14.86         0.66 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 27(12P13.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        14.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       20.12        19.66        16.24        24.92        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        21.01        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-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-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-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64        13.41         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-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-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       43.07        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.52         2.79         5.98         5.59         1.32         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       26.99        17.29         6.64        14.76        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 
       17.95        17.23        12.72        37.74         8.45        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        65.98        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-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        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         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        31.00        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.97        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24       129.27        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.28        55.76        47.08 

  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                         78.08                         140.38 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                        16.310                         18.015 
[1] "0.1 - 78.1 (16.3)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "1.6"
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    57  29
  DEL PEAK 27(12P13.1) WILD-TYPE 381 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     57   29
  DEL PEAK 27(12P13.1) WILD-TYPE  381  133
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  COLON                            57                            381
  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        13        0        5        17         1
  DEL PEAK 27(12P13.1) WILD-TYPE      89        1       31       154         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.1) MUTATED           0         2          5         12
  DEL PEAK 27(12P13.1) WILD-TYPE         3        24         16         66
                                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         41       50        19         2
D54V4, multiclass
            clus
vv           DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            17                            154
  STAGE IIB                             1                              9
  STAGE IIC                             0                              3
  STAGE III                             2                             24
  STAGE IIIA                            5                             16
  STAGE IIIB                           12                             66
  STAGE IIIC                           12                             41
  STAGE IV                             11                             50
  STAGE IVA                             8                             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 27(12P13.1) MUTATED     4  13  65   7
  DEL PEAK 27(12P13.1) WILD-TYPE  16  92 347  58
D54V5, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  T1                            4                             16
  T2                           13                             92
  T3                           65                            347
  T4                            7                             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 27(12P13.1) MUTATED    40  31  18
  DEL PEAK 27(12P13.1) WILD-TYPE 301 117  94
D54V6, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  N0                           40                            301
  N1                           31                            117
  N2                           18                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 27(12P13.1) MUTATED    56  17   2   0  13
  DEL PEAK 27(12P13.1) WILD-TYPE 390  57   8   2  50
D54V7, multiclass
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  M0                            56                            390
  M1                            17                             57
  M1A                            2                              8
  M1B                            0                              2
  MX                            13                             50
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    43  46
  DEL PEAK 27(12P13.1) WILD-TYPE 240 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     43   46
  DEL PEAK 27(12P13.1) WILD-TYPE  240  275
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  FEMALE                           43                            240
  MALE                             46                            275
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                     55
  DEL PEAK 27(12P13.1) WILD-TYPE                  323
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                               2
  DEL PEAK 27(12P13.1) WILD-TYPE                            57
                                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
D54V9, multiclass
                                clus
vv                               DEL PEAK 27(12P13.1) MUTATED
  COLON ADENOCARCINOMA                                     55
  COLON MUCINOUS ADENOCARCINOMA                             2
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 27(12P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      323
  COLON MUCINOUS ADENOCARCINOMA                              57
  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"
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED     2  87
  DEL PEAK 27(12P13.1) WILD-TYPE   7 508
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED      2   87
  DEL PEAK 27(12P13.1) WILD-TYPE    7  508
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  NO                             2                              7
  YES                           87                            508
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.1) MUTATED    64   1   6   4
  DEL PEAK 27(12P13.1) WILD-TYPE 372   4  30  25
D54V11, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  R0                           64                            372
  R1                            1                              4
  R2                            6                             30
  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                           8    51
  DEL PEAK 27(12P13.1) WILD-TYPE                        48   241
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 27(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       241
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 28(12Q21.33) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(12Q21.33) MUTATED    65  20
  DEL PEAK 28(12Q21.33) WILD-TYPE 401  89
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             85                             490 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             20                              89 
$`DEL PEAK 28(12Q21.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       37.02        17.79        34.65        36.53        30.44        23.61 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3542 
       20.28        61.84        52.44         9.63        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3673 
       14.01        33.99        13.02        17.95        23.01        50.04 
TCGA-AA-3685 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 
       37.05        31.07        17.03        24.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 
       50.99        24.00        32.02        33.04         2.96         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5256 
        1.02         0.43        14.50         0.20         3.19         2.14 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 
        0.26        48.20         8.02        29.06         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6533 
       29.03        15.02        11.01        13.05        11.08         1.32 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 
       13.41        11.38        12.59         7.50        13.38        16.24 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL 
       61.87        36.72        36.00         5.49         6.64        30.28 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3593 
       43.04        12.72        14.50        15.39        36.03        34.03 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A014 
       29.98        32.98        48.03        36.03        23.01        15.95 
TCGA-AG-A032 TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DE TCGA-DY-A1DF 
       38.04         0.49        13.97         7.10       129.27        24.13 
TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6812 
       17.00        16.31        16.41        11.51        14.86         0.66 
TCGA-G5-6233 
       18.28 

$`DEL PEAK 28(12Q21.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        16.04        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 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-A565 TCGA-A6-A566 TCGA-AA-3488 
       23.87        20.12        19.66        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        24.00        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01        24.00        20.98        34.03         2.01        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-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       14.99        12.99        13.02        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32       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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        74.56        43.07        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        26.43        22.09 
TCGA-G4-6322 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 
       47.15        52.80         4.11        10.98        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         1.32         5.19        26.99        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       14.76        67.00        24.13        17.95        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       19.10        37.74        10.39         8.45        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        65.98        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-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       19.99        19.99         7.99         0.99         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        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-A02X TCGA-AH-6547 
       49.97         1.94        38.96        61.97        41.00         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69        16.34         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         129.27                          140.38 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         17.000                          17.965 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.4"
D55V2, continuous
D55V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    60  27
  DEL PEAK 28(12Q21.33) WILD-TYPE 378 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     60   27
  DEL PEAK 28(12Q21.33) WILD-TYPE  378  135
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON                             60                             378
  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      87        1       33       152         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         17         67
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(12Q21.33) MUTATED           14       10         4         1
  DEL PEAK 28(12Q21.33) WILD-TYPE         39       51        23         1
D55V4, multiclass
            clus
vv           DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  STAGE I                               15                              87
  STAGE IA                               0                               1
  STAGE II                               3                              33
  STAGE IIA                             19                             152
  STAGE IIB                              1                               9
  STAGE IIC                              2                               1
  STAGE III                              1                              25
  STAGE IIIA                             4                              17
  STAGE IIIB                            11                              67
  STAGE IIIC                            14                              39
  STAGE IV                              10                              51
  STAGE IVA                              4                              23
  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  64   6
  DEL PEAK 28(12Q21.33) WILD-TYPE  17  90 348  59
D55V5, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  T1                             3                              17
  T2                            15                              90
  T3                            64                             348
  T4                             6                              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 28(12Q21.33) MUTATED    41  24  23
  DEL PEAK 28(12Q21.33) WILD-TYPE 300 124  89
D55V6, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  N0                            41                             300
  N1                            24                             124
  N2                            23                              89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 28(12Q21.33) MUTATED    61  13   1   1  10
  DEL PEAK 28(12Q21.33) WILD-TYPE 385  61   9   1  53
D55V7, multiclass
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  M0                             61                             385
  M1                             13                              61
  M1A                             1                               9
  M1B                             1                               1
  MX                             10                              53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    39  49
  DEL PEAK 28(12Q21.33) WILD-TYPE 244 272
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     39   49
  DEL PEAK 28(12Q21.33) WILD-TYPE  244  272
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  FEMALE                            39                             244
  MALE                              49                             272
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                     57
  DEL PEAK 28(12Q21.33) WILD-TYPE                  321
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                               2
  DEL PEAK 28(12Q21.33) WILD-TYPE                            57
                                 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
D55V9, multiclass
                                clus
vv                               DEL PEAK 28(12Q21.33) MUTATED
  COLON ADENOCARCINOMA                                      57
  COLON MUCINOUS ADENOCARCINOMA                              2
  RECTAL ADENOCARCINOMA                                     26
  RECTAL MUCINOUS ADENOCARCINOMA                             1
                                clus
vv                               DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       321
  COLON MUCINOUS ADENOCARCINOMA                               57
  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"
D55V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED     2  86
  DEL PEAK 28(12Q21.33) WILD-TYPE   7 509
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED      2   86
  DEL PEAK 28(12Q21.33) WILD-TYPE    7  509
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  NO                              2                               7
  YES                            86                             509
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(12Q21.33) MUTATED    70   0   3   3
  DEL PEAK 28(12Q21.33) WILD-TYPE 366   5  33  26
D55V11, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  R0                            70                             366
  R1                             0                               5
  R2                             3                              33
  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                           8    47
  DEL PEAK 28(12Q21.33) WILD-TYPE                        48   245
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 28(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       47
                                  clus
vv                                 DEL PEAK 28(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     48
  WHITE                                                        245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 29(14Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(14Q11.2) MUTATED   162  36
  DEL PEAK 29(14Q11.2) WILD-TYPE 304  73
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           198                            377 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                            36                             73 
$`DEL PEAK 29(14Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       37.02        42.28        35.11        15.52        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 
       14.53        32.45        32.91        30.44        23.61        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3517 
       20.28        61.84         5.03         1.02         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
        9.07        24.03        36.03        19.07        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       23.01        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 
       50.04        47.01        37.05        19.00        85.05         0.99 
TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3867 
       25.02        36.95        37.02        17.03        17.03        24.03 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       18.05        12.99        34.03        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
       34.06        26.01         7.96        34.03        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K 
       42.02        14.99        21.99        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 
       33.04        26.01         2.96         2.01        40.96         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
        1.02         0.10         0.43        14.50         0.95        15.75 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 
        5.52         6.87        75.25         1.41         5.65        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 
       29.56         5.23         1.94         3.06         2.14         0.07 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 
        0.26        48.20         2.01         8.02         8.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.04        29.03        13.02        15.02        11.01        11.08 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 
       10.06        14.99        12.26        13.51        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 
       15.12        14.30        13.41        11.38        38.20        12.59 
TCGA-DM-A1D9 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 
      140.38         6.12        14.04       119.93        13.38        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       33.67         1.28         0.53        28.21         8.35        82.39 
TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 
       36.72        91.79         4.11        10.52         5.59         5.19 
TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
        5.49        30.28        17.95        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 
       37.74        10.39        65.98        11.84        36.03         7.07 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3882 
       34.03        50.04         6.05         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02        17.03        35.01         1.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 
       14.04        17.03         6.02        25.97        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04         0.49        10.19         6.05         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        13.97         7.99        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        36.00         7.10        13.05        10.06       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 
       24.13        51.48        20.55        20.91        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 
       16.31        16.41        10.78        11.97        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.02         0.66         0.76        18.28        55.76        26.43 

$`DEL PEAK 29(14Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       17.79        44.91        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       16.04        31.63        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        29.16        27.09         8.38        25.18        24.16 
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        52.44 
TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         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-3522 
       58.03        63.98         1.02        13.02         1.02        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        8.05        19.07        29.00        29.00        26.01        12.99 
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-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       29.95        20.98        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-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
        0.99         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-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 
        0.99        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         4.21        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
        0.20        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.25         3.29         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-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        11.51        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-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        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
        1.55        16.31        16.24        35.41        19.43       107.67 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       55.04        51.75        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80        10.98         2.79         5.98 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        1.32        26.99        17.29         6.64        14.76        67.00 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       24.13        17.23        43.04        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        86.63        12.00        32.02         8.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        46.03         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
       29.98         1.02        32.98         0.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4022 
       14.01        48.03        32.02        19.99         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        13.94        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 
        0.72         4.60         1.81         6.97        60.03        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       19.96        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        37.51        14.86 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        0.69         0.53         1.12         0.46        47.08 

  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        16.375                         19.000 
[1] "0.1 - 140.4 (16.4)" "0.1 - 139.2 (19.0)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   135  68
  DEL PEAK 29(14Q11.2) WILD-TYPE 303  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    135   68
  DEL PEAK 29(14Q11.2) WILD-TYPE  303   94
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON                           135                            303
  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        55         1
  DEL PEAK 29(14Q11.2) WILD-TYPE      70        1       25       116         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q11.2) MUTATED           1         9          9         28
  DEL PEAK 29(14Q11.2) WILD-TYPE         2        17         12         50
                                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         35       36        15         2
D56V4, multiclass
            clus
vv           DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  STAGE I                              32                             70
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            55                            116
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             9                             17
  STAGE IIIA                            9                             12
  STAGE IIIB                           28                             50
  STAGE IIIC                           18                             35
  STAGE IV                             25                             36
  STAGE IVA                            12                             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 29(14Q11.2) MUTATED     9  33 147  17
  DEL PEAK 29(14Q11.2) WILD-TYPE  11  72 265  48
D56V5, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           33                             72
  T3                          147                            265
  T4                           17                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 29(14Q11.2) MUTATED   106  63  37
  DEL PEAK 29(14Q11.2) WILD-TYPE 235  85  75
D56V6, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  N0                          106                            235
  N1                           63                             85
  N2                           37                             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 29(14Q11.2) MUTATED   146  34   3   0  20
  DEL PEAK 29(14Q11.2) WILD-TYPE 300  40   7   2  43
D56V7, multiclass
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  M0                           146                            300
  M1                            34                             40
  M1A                            3                              7
  M1B                            0                              2
  MX                            20                             43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED    97 109
  DEL PEAK 29(14Q11.2) WILD-TYPE 186 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED     97  109
  DEL PEAK 29(14Q11.2) WILD-TYPE  186  212
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  FEMALE                           97                            186
  MALE                            109                            212
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                    129
  DEL PEAK 29(14Q11.2) WILD-TYPE                  249
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                               5
  DEL PEAK 29(14Q11.2) WILD-TYPE                            54
                                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
D56V9, multiclass
                                clus
vv                               DEL PEAK 29(14Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    129
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      249
  COLON MUCINOUS ADENOCARCINOMA                              54
  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"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED     4 202
  DEL PEAK 29(14Q11.2) WILD-TYPE   5 393
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED      4  202
  DEL PEAK 29(14Q11.2) WILD-TYPE    5  393
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  NO                             4                              5
  YES                          202                            393
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(14Q11.2) MUTATED   145   2  10  10
  DEL PEAK 29(14Q11.2) WILD-TYPE 291   3  26  19
D56V11, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  R0                          145                            291
  R1                            2                              3
  R2                           10                             26
  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                          19   101
  DEL PEAK 29(14Q11.2) WILD-TYPE                        37   191
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     101
                                  clus
vv                                 DEL PEAK 29(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 30(14Q31.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(14Q31.1) MUTATED   166  35
  DEL PEAK 30(14Q31.1) WILD-TYPE 300  74
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           201                            374 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                            35                             74 
$`DEL PEAK 30(14Q31.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 
       37.02        42.28        35.11        45.60        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       36.53        14.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13        25.08        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 
       24.69        23.87        20.28        61.84         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        24.03        19.07        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       13.02        23.01        13.94        19.99         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       50.04        47.01        15.02        37.05        19.00        85.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3860 
        0.99        25.02        36.95        37.02        17.03        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 
       17.03        24.03        18.05         2.01        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       21.99        16.08        50.99        34.06        26.01        24.00 
TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z 
        7.96        17.03        27.02        42.02        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        32.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        2.01        40.96         1.58         1.02         0.10         0.43 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       14.50         0.95        15.75         0.20         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
       75.25         1.41         5.65        22.36        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 
        1.94         3.06         2.14         0.07         0.26        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        2.01         8.02         8.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       13.02        15.02        13.05        11.08        10.06        14.99 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       12.26        13.51        18.25         1.32        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       13.41        11.38        38.20        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6806 
      131.51        14.04       119.93       117.07        13.38        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
       33.67         1.28         0.53         8.35        82.39        36.72 
TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       91.79         4.11        10.52         5.59         5.19         5.49 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-A56L TCGA-AF-A56N 
       30.28        17.95        13.55        37.74        65.98        11.84 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
        0.99         1.02         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C 
        1.02        48.03        36.03        14.04        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       25.97        23.01        70.03         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
        0.49        10.19         6.05         6.05         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       13.97         7.99        10.98        11.01        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00         7.10        13.05        10.06       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-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         1.02         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-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       17.79        44.91        13.94        37.05        37.25        16.04 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       29.16        27.09         8.38        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       19.66        16.24        24.92        52.44         9.63         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 
       63.98         1.02        13.02         1.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
       54.02         0.92        47.05        11.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 
        1.02        17.98        15.95        38.99        14.93         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07        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         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-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         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
       50.37        58.39        32.94         5.13        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74         3.19         2.24         3.25         3.29         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        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        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-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-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       11.08        11.01        12.03        19.59        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       12.59        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       26.47        81.37        35.97        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
        1.55        16.31        16.24        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       26.17        46.75        47.15        52.80        10.98         2.79 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.98         1.32        26.99        17.29         6.64        14.76 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       67.00        24.13        17.23        43.04        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       86.63        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 
        2.01        24.00         1.02         2.01         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 
       19.99        19.99         7.99        29.98        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       19.99        36.95        13.02        14.01        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
       28.04         1.02         0.99        20.98        13.94        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
        1.45         0.69         0.72         4.60         1.81         6.97 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       60.03        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-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        37.51        14.86         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6572 
        0.46        47.08 

  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        16.080                         19.085 
[1] "0.1 - 140.4 (16.1)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   142  68
  DEL PEAK 30(14Q31.1) WILD-TYPE 296  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    142   68
  DEL PEAK 30(14Q31.1) WILD-TYPE  296   94
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON                           142                            296
  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        58         1
  DEL PEAK 30(14Q31.1) WILD-TYPE      70        1       27       113         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(14Q31.1) MUTATED           1        10          9         29
  DEL PEAK 30(14Q31.1) WILD-TYPE         2        16         12         49
                                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         34       34        15         1
D57V4, multiclass
            clus
vv           DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  STAGE I                              32                             70
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            58                            113
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            9                             12
  STAGE IIIB                           29                             49
  STAGE IIIC                           19                             34
  STAGE IV                             27                             34
  STAGE IVA                            12                             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 30(14Q31.1) MUTATED     9  33 153  17
  DEL PEAK 30(14Q31.1) WILD-TYPE  11  72 259  48
D57V5, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  T1                            9                             11
  T2                           33                             72
  T3                          153                            259
  T4                           17                             48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 30(14Q31.1) MUTATED   107  64  41
  DEL PEAK 30(14Q31.1) WILD-TYPE 234  84  71
D57V6, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  N0                          107                            234
  N1                           64                             84
  N2                           41                             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 30(14Q31.1) MUTATED   150  37   3   1  18
  DEL PEAK 30(14Q31.1) WILD-TYPE 296  37   7   1  45
D57V7, multiclass
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  M0                           150                            296
  M1                            37                             37
  M1A                            3                              7
  M1B                            1                              1
  MX                            18                             45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED    94 118
  DEL PEAK 30(14Q31.1) WILD-TYPE 189 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED     94  118
  DEL PEAK 30(14Q31.1) WILD-TYPE  189  203
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  FEMALE                           94                            189
  MALE                            118                            203
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                    136
  DEL PEAK 30(14Q31.1) WILD-TYPE                  242
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                               5
  DEL PEAK 30(14Q31.1) WILD-TYPE                            54
                                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
D57V9, multiclass
                                clus
vv                               DEL PEAK 30(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    136
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      242
  COLON MUCINOUS ADENOCARCINOMA                              54
  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"
D57V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED     2 210
  DEL PEAK 30(14Q31.1) WILD-TYPE   7 385
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED      2  210
  DEL PEAK 30(14Q31.1) WILD-TYPE    7  385
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  NO                             2                              7
  YES                          210                            385
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(14Q31.1) MUTATED   145   2  15  10
  DEL PEAK 30(14Q31.1) WILD-TYPE 291   3  21  19
D57V11, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  R0                          145                            291
  R1                            2                              3
  R2                           15                             21
  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                          20   100
  DEL PEAK 30(14Q31.1) WILD-TYPE                        36   192
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 30(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     100
                                  clus
vv                                 DEL PEAK 30(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 31(15Q11.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q11.2) MUTATED   189  44
  DEL PEAK 31(15Q11.2) WILD-TYPE 277  65
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           233                            342 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                            44                             65 
$`DEL PEAK 31(15Q11.2) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 
       43.76        43.43        17.79        42.28        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       15.52        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       29.19        29.16        22.52        25.08        20.61        21.76 
TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.12        20.28        61.84        52.44         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
        1.02         6.97        37.05        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 
       19.99         2.01        50.04        47.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05         1.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       24.03        27.02        29.98        12.99         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        32.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       41.00         1.58         1.02         0.10         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31         0.95        15.75         5.52         6.87 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79        61.41        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 
        3.19         2.14         0.26         1.35       102.44        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 
        2.01         8.02        27.02        13.02        29.06         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        16.04        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       12.26        20.19        17.75         1.32        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 
       12.49         7.53        10.13         9.04        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
        6.12        14.04        35.97        95.18        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       28.21         8.35        43.07        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       36.72        36.00        91.79        46.75        10.98        10.52 
TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
        1.32        30.28        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         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
        2.01        46.03        34.03         6.05        19.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
        0.99        19.99        17.03        35.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        14.04        17.03        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       37.02         1.02        12.00        64.01         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       41.00        38.04         0.49         0.69        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        9.37         4.73         7.99        12.99        13.97        36.00 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       13.05        10.06        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       51.48         0.49         2.40        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 31(15Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 
        5.06         5.26        37.02        46.65        23.38        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 
       13.94        37.05        37.25        16.04        14.53        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 
       23.87        19.66        16.24        24.92         9.63         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
        0.99        17.95        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 
       17.98        15.95        14.93        33.07        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       53.00        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
        0.99        21.99        34.98         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.20        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.07         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 
       23.05        20.02        37.02        26.04         8.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.95        14.99        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        18.25         7.92        17.85         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       38.20        49.91        44.32       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        13.64        13.45         6.18        16.31 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       29.59        19.43       107.67        82.39        23.51        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80         4.11         2.79         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       17.95        17.23        19.10        12.72        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       15.39        20.02        86.63        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98         0.99         1.02        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02        36.03         1.02         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
        6.02        15.95        36.03         9.07        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.05         6.97        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       10.98        11.01        15.02        12.00        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 
       30.05        12.95         5.29       126.44        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.34        17.46         8.45         9.96        37.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                         17.75                          17.90 
[1] "0.1 - 140.4 (17.8)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   169  74
  DEL PEAK 31(15Q11.2) WILD-TYPE 269  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    169   74
  DEL PEAK 31(15Q11.2) WILD-TYPE  269   88
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  COLON                           169                            269
  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        38        0        9        63         3
  DEL PEAK 31(15Q11.2) WILD-TYPE      64        1       27       108         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q11.2) MUTATED           2         8         12         33
  DEL PEAK 31(15Q11.2) WILD-TYPE         1        18          9         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q11.2) MUTATED           27       30        14         2
  DEL PEAK 31(15Q11.2) WILD-TYPE         26       31        13         0
D58V4, multiclass
            clus
vv           DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  STAGE I                              38                             64
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            63                            108
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                             8                             18
  STAGE IIIA                           12                              9
  STAGE IIIB                           33                             45
  STAGE IIIC                           27                             26
  STAGE IV                             30                             31
  STAGE IVA                            14                             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 31(15Q11.2) MUTATED     9  39 173  25
  DEL PEAK 31(15Q11.2) WILD-TYPE  11  66 239  40
D58V5, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           39                             66
  T3                          173                            239
  T4                           25                             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 31(15Q11.2) MUTATED   122  71  53
  DEL PEAK 31(15Q11.2) WILD-TYPE 219  77  59
D58V6, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  N0                          122                            219
  N1                           71                             77
  N2                           53                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 31(15Q11.2) MUTATED   174  37   6   2  23
  DEL PEAK 31(15Q11.2) WILD-TYPE 272  37   4   0  40
D58V7, multiclass
     clus
vv    DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  M0                           174                            272
  M1                            37                             37
  M1A                            6                              4
  M1B                            2                              0
  MX                            23                             40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   110 136
  DEL PEAK 31(15Q11.2) WILD-TYPE 173 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    110  136
  DEL PEAK 31(15Q11.2) WILD-TYPE  173  185
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  FEMALE                          110                            173
  MALE                            136                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                    153
  DEL PEAK 31(15Q11.2) WILD-TYPE                  225
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              15
  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
D58V9, multiclass
                                clus
vv                               DEL PEAK 31(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    153
  COLON MUCINOUS ADENOCARCINOMA                            15
  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"
D58V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED     7 239
  DEL PEAK 31(15Q11.2) WILD-TYPE   2 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED      7  239
  DEL PEAK 31(15Q11.2) WILD-TYPE    2  356
     clus
vv    DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  NO                             7                              2
  YES                          239                            356
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q11.2) MUTATED   174   2  15   9
  DEL PEAK 31(15Q11.2) WILD-TYPE 262   3  21  20
D58V11, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  R0                          174                            262
  R1                            2                              3
  R2                           15                             21
  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                          19   127
  DEL PEAK 31(15Q11.2) WILD-TYPE                        37   165
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     127
                                  clus
vv                                 DEL PEAK 31(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       165
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 32(15Q15.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q15.2) MUTATED   187  43
  DEL PEAK 32(15Q15.2) WILD-TYPE 279  66
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           230                            345 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                            43                             66 
$`DEL PEAK 32(15Q15.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       44.91        45.60        15.52        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.91        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        20.12        20.28        61.84        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 
        5.03         1.02         1.02         6.97         9.07        37.05 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
       23.01        19.99        19.99         2.01        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
       11.01        37.05        19.00        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
        0.99        31.07        17.03        24.03        29.98        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 
        2.01        21.99        50.99        13.05        34.06        24.00 
TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       16.31         0.95        15.75         0.20         5.52         6.87 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79        61.41        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 
        3.19         2.14         0.26       102.44        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
        8.02        27.02        13.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 
       17.03        14.04        29.03        16.04        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       20.19         1.32        15.12         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       13.41        11.38       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 
      140.38       131.51         6.12        35.97        95.18        13.38 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       35.41        28.21         8.35        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       36.72        36.00        26.04        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       10.52         1.32        30.28        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-3593 TCGA-AG-3600 
        1.02         2.01        24.00        46.03        34.03         6.05 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
       19.99         0.99        29.98        32.98         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 
        0.69        10.19         6.05         9.37         4.73         7.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       12.99        13.97        36.00        13.05        10.06        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 
       57.24        24.13        51.48         0.49         2.40        15.85 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       11.97        31.30        14.86         1.02         0.66         0.69 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 32(15Q15.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
        5.26        46.65        23.38        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       37.25        16.04        14.53        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        23.87        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       16.24        24.92         9.63         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        1.02        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 
       34.03        29.00        29.00        26.01         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
        6.97        54.02        14.01         0.92        47.05        15.02 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.98         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        32.05        31.07        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 
        2.01        20.98        34.03        16.08        26.01        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.46         0.92        27.09        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02        37.02        26.04         8.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       14.04        11.01        12.95        14.99        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA 
       10.26       119.70        24.43        38.20        49.91         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64        13.45         6.18        16.31        29.59 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        82.39        23.51        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
        4.11         2.79         5.98         5.59         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       26.99        17.29         6.64        14.76        67.00        17.95 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.23        19.10        12.72        10.39         8.45        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-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       19.99         7.99         1.02         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       13.02        14.01        48.03        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.98         6.02        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         1.45         0.72         4.60         1.81         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.97        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       12.00        15.02         7.10        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      126.44       129.27        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 
       17.00        18.28        17.69        16.34        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        9.96        37.51         0.39         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                         17.03                          17.95 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   163  77
  DEL PEAK 32(15Q15.2) WILD-TYPE 275  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    163   77
  DEL PEAK 32(15Q15.2) WILD-TYPE  275   85
        clus
vv       DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  COLON                           163                            275
  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        39        0        8        60         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         9         10         33
  DEL PEAK 32(15Q15.2) WILD-TYPE         1        17         11         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q15.2) MUTATED           26       33        13         2
  DEL PEAK 32(15Q15.2) WILD-TYPE         27       28        14         0
D59V4, multiclass
            clus
vv           DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  STAGE I                              39                             63
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            60                            111
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                             9                             17
  STAGE IIIA                           10                             11
  STAGE IIIB                           33                             45
  STAGE IIIC                           26                             27
  STAGE IV                             33                             28
  STAGE IVA                            13                             14
  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  39 171  24
  DEL PEAK 32(15Q15.2) WILD-TYPE  11  66 241  41
D59V5, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  T1                            9                             11
  T2                           39                             66
  T3                          171                            241
  T4                           24                             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 32(15Q15.2) MUTATED   118  74  51
  DEL PEAK 32(15Q15.2) WILD-TYPE 223  74  61
D59V6, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  N0                          118                            223
  N1                           74                             74
  N2                           51                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 32(15Q15.2) MUTATED   167  39   6   2  24
  DEL PEAK 32(15Q15.2) WILD-TYPE 279  35   4   0  39
D59V7, multiclass
     clus
vv    DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  M0                           167                            279
  M1                            39                             35
  M1A                            6                              4
  M1B                            2                              0
  MX                            24                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   107 136
  DEL PEAK 32(15Q15.2) WILD-TYPE 176 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    107  136
  DEL PEAK 32(15Q15.2) WILD-TYPE  176  185
        clus
vv       DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  FEMALE                          107                            176
  MALE                            136                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                    148
  DEL PEAK 32(15Q15.2) WILD-TYPE                  230
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                              14
  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
D59V9, multiclass
                                clus
vv                               DEL PEAK 32(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                    148
  COLON MUCINOUS ADENOCARCINOMA                            14
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 32(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      230
  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"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED     7 236
  DEL PEAK 32(15Q15.2) WILD-TYPE   2 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED      7  236
  DEL PEAK 32(15Q15.2) WILD-TYPE    2  359
     clus
vv    DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  NO                             7                              2
  YES                          236                            359
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q15.2) MUTATED   174   2  16   8
  DEL PEAK 32(15Q15.2) WILD-TYPE 262   3  20  21
D59V11, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  R0                          174                            262
  R1                            2                              3
  R2                           16                             20
  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                          20   124
  DEL PEAK 32(15Q15.2) WILD-TYPE                        36   168
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     124
                                  clus
vv                                 DEL PEAK 32(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 33(15Q21.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q21.1) MUTATED   187  40
  DEL PEAK 33(15Q21.1) WILD-TYPE 279  69
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           227                            348 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                            40                             69 
$`DEL PEAK 33(15Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       37.02        43.76        43.43        23.38        17.79        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       45.60        15.52        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 
       30.44        29.19        29.16        22.52        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       21.76        20.12        20.28        61.84         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        1.02         6.97         9.07        37.05        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       19.99        19.99         2.01        50.04        47.01        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 
       37.05        19.00        36.00        85.05        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 
       31.07        17.03        24.03        29.98        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 
       21.99        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        30.02        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 
       15.75         0.20         5.52         6.87        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 
       62.79        61.41        29.56         5.23         3.19         2.14 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 
        0.26       102.44        48.20         2.01         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       13.02        29.06         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       29.03        16.04        15.02        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 
       11.01        10.06        12.03        12.26        20.19         1.32 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       15.12         7.53        10.13         9.04        13.41        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        13.32        12.59       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        6.12        35.97        95.18        13.38        35.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       16.24        33.67         1.28         0.53        35.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       61.87        55.04        45.11        36.72        36.00        26.04 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-RU-A8FL 
       91.79        46.75        10.98        10.52         1.32        30.28 
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         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       46.03        34.03         6.05        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       32.98         0.99        19.99        17.03        35.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        14.04        17.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         1.02        12.00         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       41.00        38.04         0.49         0.69        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        9.37         4.73         7.99        12.99        13.97        36.00 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       13.05        10.06        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        0.49         2.40        15.85        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 33(15Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 
        5.06         5.26        46.65        42.28        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        16.04        14.53        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 
       19.66        16.24        24.92        52.44         9.63         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       15.95        14.93        32.05        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 
       24.00         2.01        20.98        34.03        16.08        26.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.19        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94         5.13        22.36        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       12.10       100.01        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04         8.02        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        12.00        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 
       12.99        13.02        14.04        11.01        12.95        14.99 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        13.51        11.51        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31        29.59        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        43.07        53.62        44.68        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       39.42        35.93        26.43        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        47.15        52.80         4.11         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 
       14.76        67.00        17.95        17.23        19.10        12.72 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 
       10.39         8.45        15.39        20.02        86.63        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       12.00         8.02         7.07         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 
       12.03         0.99        15.95        19.99         7.99         1.02 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 
        0.99         1.02        36.95        13.02        14.01        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       32.02        36.03         1.02         0.99        20.98         6.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.05         6.97        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       10.98        11.01        15.02        12.00        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       30.05        12.95         5.29       126.44       129.27        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.34        17.46         8.45         9.96        37.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        17.790                         17.835 
[1] "0.1 - 140.4 (17.8)" "0.1 - 139.2 (17.8)"
[1] "hr=" "1.1"
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   162  77
  DEL PEAK 33(15Q21.1) WILD-TYPE 276  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    162   77
  DEL PEAK 33(15Q21.1) WILD-TYPE  276   85
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  COLON                           162                            276
  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        37        0        8        63         4
  DEL PEAK 33(15Q21.1) WILD-TYPE      65        1       28       108         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q21.1) MUTATED           2         9         10         31
  DEL PEAK 33(15Q21.1) WILD-TYPE         1        17         11         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q21.1) MUTATED           25       32        13         2
  DEL PEAK 33(15Q21.1) WILD-TYPE         28       29        14         0
D60V4, multiclass
            clus
vv           DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  STAGE I                              37                             65
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            63                            108
  STAGE IIB                             4                              6
  STAGE IIC                             2                              1
  STAGE III                             9                             17
  STAGE IIIA                           10                             11
  STAGE IIIB                           31                             47
  STAGE IIIC                           25                             28
  STAGE IV                             32                             29
  STAGE IVA                            13                             14
  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  38 170  25
  DEL PEAK 33(15Q21.1) WILD-TYPE  12  67 242  40
D60V5, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  T1                            8                             12
  T2                           38                             67
  T3                          170                            242
  T4                           25                             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 33(15Q21.1) MUTATED   120  71  50
  DEL PEAK 33(15Q21.1) WILD-TYPE 221  77  62
D60V6, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  N0                          120                            221
  N1                           71                             77
  N2                           50                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 33(15Q21.1) MUTATED   167  38   6   2  24
  DEL PEAK 33(15Q21.1) WILD-TYPE 279  36   4   0  39
D60V7, multiclass
     clus
vv    DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  M0                           167                            279
  M1                            38                             36
  M1A                            6                              4
  M1B                            2                              0
  MX                            24                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   105 136
  DEL PEAK 33(15Q21.1) WILD-TYPE 178 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    105  136
  DEL PEAK 33(15Q21.1) WILD-TYPE  178  185
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  FEMALE                          105                            178
  MALE                            136                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                    147
  DEL PEAK 33(15Q21.1) WILD-TYPE                  231
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                              14
  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
D60V9, multiclass
                                clus
vv                               DEL PEAK 33(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    147
  COLON MUCINOUS ADENOCARCINOMA                            14
  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"
D60V10, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED     7 234
  DEL PEAK 33(15Q21.1) WILD-TYPE   2 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED      7  234
  DEL PEAK 33(15Q21.1) WILD-TYPE    2  361
     clus
vv    DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  NO                             7                              2
  YES                          234                            361
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q21.1) MUTATED   173   1  16   8
  DEL PEAK 33(15Q21.1) WILD-TYPE 263   4  20  21
D60V11, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  R0                          173                            263
  R1                            1                              4
  R2                           16                             20
  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                          17   122
  DEL PEAK 33(15Q21.1) WILD-TYPE                        39   170
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     122
                                  clus
vv                                 DEL PEAK 33(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 34(15Q22.33) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 34(15Q22.33) MUTATED   179  41
  DEL PEAK 34(15Q22.33) WILD-TYPE 287  68
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            220                             355 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                             41                              68 
$`DEL PEAK 34(15Q22.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 
       37.02        43.76        43.43        17.79        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       15.52        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 
       29.16        22.52        25.08        20.61        21.76        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         1.02         1.02         6.97         9.07 
TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       37.05        29.00        12.99        33.99        21.01        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       23.01        19.99        19.99         2.01        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       19.00        36.00        85.05        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       17.03         0.99         0.99        31.07        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       29.98        12.99         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       34.06        24.00        27.02        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T 
       17.03        14.99        15.02        15.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       26.01         2.96        41.00         1.58         1.02         0.10 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         0.46        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        0.20         5.52         6.87        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       61.41        29.56         5.23         3.19         2.14         0.26 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
      102.44        48.20         2.01         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       16.04        15.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       12.03        20.19         1.32        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        6.12        14.04        95.18        13.38        35.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       16.24        33.67         1.28         0.53        35.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       61.87        55.04        45.11        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       46.75        10.98        10.52         1.32         6.64        30.28 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        43.04        13.55        12.72        37.74        14.50 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       10.39        65.98        32.02         1.02         2.01        24.00 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 
       34.03         6.05        15.95        19.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
       19.99        17.03        35.01         1.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       14.04        17.03        13.94        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        12.00        70.03        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 
        0.49         0.69        10.19         6.05         9.37         7.99 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       10.98        12.99        13.97        36.00        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40        15.85        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        31.30        14.86         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         0.46        18.28        26.43 

$`DEL PEAK 34(15Q22.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
        5.06         5.26        46.65        23.38        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       13.94        37.05        37.25        16.04        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       27.09        24.13         8.38        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       52.44         9.63         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       29.00        26.01         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.98        15.95        14.93        33.07        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       34.03        16.08        26.01        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 
       17.03         4.01        27.02         0.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        0.79         0.72         0.76         0.20         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
        1.41         5.65        32.94         5.13        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04         8.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 
       16.01        15.02        15.02        15.02        12.00        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       13.05        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25         7.92        17.85         4.50 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       38.20         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31        29.59        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        43.07        53.62        44.68        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80         4.11         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 
       14.76        67.00        17.95        17.23        19.10        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
        8.45        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-3594 
       12.00         8.02         7.07         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04        12.03         0.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02        32.98         0.99         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       14.01        48.03        32.02        36.03         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N 
       20.98         6.02        15.95        36.03         9.07        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       64.01        10.98        51.98        49.97         1.94        61.97 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.72         4.60         1.81         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
        4.73        13.97        60.03        11.01        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02         7.10        30.05        12.95         5.29       126.44 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       17.69        16.34         8.61        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
       37.51         0.39         0.53         1.12         0.76        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                          17.03                           18.05 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1"  
D61V2, continuous
D61V3, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   153  75
  DEL PEAK 34(15Q22.33) WILD-TYPE 285  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    153   75
  DEL PEAK 34(15Q22.33) WILD-TYPE  285   87
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  COLON                            153                             285
  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        31        0        7        60         3
  DEL PEAK 34(15Q22.33) WILD-TYPE      71        1       29       111         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q22.33) MUTATED           2         7         11         31
  DEL PEAK 34(15Q22.33) WILD-TYPE         1        19         10         47
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(15Q22.33) MUTATED           28       31        14         1
  DEL PEAK 34(15Q22.33) WILD-TYPE         25       30        13         1
D61V4, multiclass
            clus
vv           DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  STAGE I                               31                              71
  STAGE IA                               0                               1
  STAGE II                               7                              29
  STAGE IIA                             60                             111
  STAGE IIB                              3                               7
  STAGE IIC                              2                               1
  STAGE III                              7                              19
  STAGE IIIA                            11                              10
  STAGE IIIB                            31                              47
  STAGE IIIC                            28                              25
  STAGE IV                              31                              30
  STAGE IVA                             14                              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 34(15Q22.33) MUTATED     9  30 170  22
  DEL PEAK 34(15Q22.33) WILD-TYPE  11  75 242  43
D61V5, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  T1                             9                              11
  T2                            30                              75
  T3                           170                             242
  T4                            22                              43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 34(15Q22.33) MUTATED   110  68  53
  DEL PEAK 34(15Q22.33) WILD-TYPE 231  80  59
D61V6, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  N0                           110                             231
  N1                            68                              80
  N2                            53                              59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 34(15Q22.33) MUTATED   158  38   6   1  23
  DEL PEAK 34(15Q22.33) WILD-TYPE 288  36   4   1  40
D61V7, multiclass
     clus
vv    DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  M0                            158                             288
  M1                             38                              36
  M1A                             6                               4
  M1B                             1                               1
  MX                             23                              40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   103 128
  DEL PEAK 34(15Q22.33) WILD-TYPE 180 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    103  128
  DEL PEAK 34(15Q22.33) WILD-TYPE  180  193
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  FEMALE                           103                             180
  MALE                             128                             193
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                    139
  DEL PEAK 34(15Q22.33) WILD-TYPE                  239
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                              13
  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
D61V9, multiclass
                                clus
vv                               DEL PEAK 34(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                     139
  COLON MUCINOUS ADENOCARCINOMA                             13
  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"
D61V10, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED     8 223
  DEL PEAK 34(15Q22.33) WILD-TYPE   1 372
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED      8  223
  DEL PEAK 34(15Q22.33) WILD-TYPE    1  372
     clus
vv    DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  NO                              8                               1
  YES                           223                             372
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 34(15Q22.33) MUTATED   165   1  15   8
  DEL PEAK 34(15Q22.33) WILD-TYPE 271   4  21  21
D61V11, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  R0                           165                             271
  R1                             1                               4
  R2                            15                              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"
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                          17   124
  DEL PEAK 34(15Q22.33) WILD-TYPE                        39   168
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 34(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      124
                                  clus
vv                                 DEL PEAK 34(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     39
  WHITE                                                        168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 35(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16P13.3) MUTATED    43  20
  DEL PEAK 35(16P13.3) WILD-TYPE 423  89
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            63                            512 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            20                             89 
$`DEL PEAK 35(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 
       17.79        44.91        45.60        34.65        14.53        21.76 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 
       61.84         5.03        13.02        54.02        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 
       36.95        31.07         2.01        33.01         2.01         2.01 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F TCGA-AA-A02Y TCGA-AD-A5EK 
       27.02        34.03        27.02        39.98        39.98         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
        0.46        14.50        16.31         0.20         5.52         5.65 
TCGA-AZ-6607 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
        3.19        13.02        22.03        22.98         5.03        15.02 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       16.04        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 TCGA-G4-6294 TCGA-G4-6626 
       49.91        12.59        44.32         8.61        28.21        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AG-3578 TCGA-AG-3600 
        4.11        10.98        26.99        30.28        32.02         6.05 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-4005 TCGA-AG-A02G TCGA-DC-6682 TCGA-EI-6882 
       19.99         7.99        14.04        38.96        13.05         8.61 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        1.02         0.53        18.28 

$`DEL PEAK 35(16P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       23.38        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       30.02        18.05        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       26.01        37.02        39.06        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        1.58         1.02         0.10         0.76         0.20         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       27.02        29.06        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        13.32       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
        1.28         0.53        35.41        19.43       107.67         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        91.79        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       17.29         6.64        14.76        67.00        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        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-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03         1.02        17.03         0.99        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-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-A02N 
       64.01        10.98        51.98        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         61.84                         140.38 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                         16.31                          17.95 
[1] "0.2 - 61.8 (16.3)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "2.2"
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    54  13
  DEL PEAK 35(16P13.3) WILD-TYPE 384 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     54   13
  DEL PEAK 35(16P13.3) WILD-TYPE  384  149
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  COLON                            54                            384
  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        23         2
  DEL PEAK 35(16P13.3) WILD-TYPE      98        1       33       148         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         21         69
                                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         42       53        22         2
D62V4, multiclass
            clus
vv           DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  STAGE I                               4                             98
  STAGE IA                              0                              1
  STAGE II                              3                             33
  STAGE IIA                            23                            148
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             0                             26
  STAGE IIIA                            0                             21
  STAGE IIIB                            9                             69
  STAGE IIIC                           11                             42
  STAGE IV                              8                             53
  STAGE IVA                             5                             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 35(16P13.3) MUTATED     0   6  54   7
  DEL PEAK 35(16P13.3) WILD-TYPE  20  99 358  58
D62V5, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  T1                            0                             20
  T2                            6                             99
  T3                           54                            358
  T4                            7                             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 35(16P13.3) MUTATED    33  16  18
  DEL PEAK 35(16P13.3) WILD-TYPE 308 132  94
D62V6, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  N0                           33                            308
  N1                           16                            132
  N2                           18                             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 35(16P13.3) MUTATED    45  10   3   0   6
  DEL PEAK 35(16P13.3) WILD-TYPE 401  64   7   2  57
D62V7, multiclass
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  M0                            45                            401
  M1                            10                             64
  M1A                            3                              7
  M1B                            0                              2
  MX                             6                             57
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    30  37
  DEL PEAK 35(16P13.3) WILD-TYPE 253 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     30   37
  DEL PEAK 35(16P13.3) WILD-TYPE  253  284
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  FEMALE                           30                            253
  MALE                             37                            284
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                     47
  DEL PEAK 35(16P13.3) WILD-TYPE                  331
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                               7
  DEL PEAK 35(16P13.3) WILD-TYPE                            52
                                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
D62V9, multiclass
                                clus
vv                               DEL PEAK 35(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                     47
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 35(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      331
  COLON MUCINOUS ADENOCARCINOMA                              52
  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"
D62V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED     0  67
  DEL PEAK 35(16P13.3) WILD-TYPE   9 528
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED      0   67
  DEL PEAK 35(16P13.3) WILD-TYPE    9  528
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  NO                             0                              9
  YES                           67                            528
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16P13.3) MUTATED    50   1   4   1
  DEL PEAK 35(16P13.3) WILD-TYPE 386   4  32  28
D62V11, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  R0                           50                            386
  R1                            1                              4
  R2                            4                             32
  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                          10    32
  DEL PEAK 35(16P13.3) WILD-TYPE                        46   260
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 35(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 35(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    46
  WHITE                                                       260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 36(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16Q23.1) MUTATED    58  19
  DEL PEAK 36(16Q23.1) WILD-TYPE 408  90
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            77                            498 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            19                             90 
$`DEL PEAK 36(16Q23.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-5660 TCGA-A6-5661 
       37.02        23.38        42.28        45.60        29.19        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-A565 TCGA-AA-3494 
       22.06        22.52        21.76        24.39        16.24         1.02 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3672 
        6.97        13.02         1.02         0.99        21.01         0.92 
TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       37.05        17.98        38.99        36.03        31.07        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A01P 
       33.01         2.01        21.99        30.02        18.05        38.07 
TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-A5EK TCGA-AY-A69D 
        1.02         2.96        22.03        41.00         0.43         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5254 
        5.65         5.13        49.41        12.10         3.19         2.24 
TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6678 
        3.29        22.03         5.03        15.02        13.02        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-NH-A50T 
       20.19        17.75        15.12        24.43         7.50         4.11 
TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 
       10.98        14.76        30.28        10.39        32.02         1.02 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-4005 
        6.05        19.99         7.99        32.98         1.02        14.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 
        0.49         0.72        13.05       129.27        11.51        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        8.45         9.96         1.02         0.53        18.28 

$`DEL PEAK 36(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        46.65        43.76        43.43        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       31.63        30.44        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        23.87        20.12        19.66        20.28 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        15.95        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         1.58         1.02         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        62.79        61.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        18.25         1.32         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-WS-AB45 TCGA-AF-2687 
        5.49        26.99        17.29         6.64        67.00        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
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-3593 
        7.07         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-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         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30        14.86         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         0.46        55.76        47.08        26.43 

  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                        129.27                         140.38 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                         14.76                          18.05 
[1] "0.4 - 129.3 (14.8)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.9"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    58  23
  DEL PEAK 36(16Q23.1) WILD-TYPE 380 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     58   23
  DEL PEAK 36(16Q23.1) WILD-TYPE  380  139
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  COLON                            58                            380
  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        24         2
  DEL PEAK 36(16Q23.1) WILD-TYPE      89        1       31       147         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         21         70
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(16Q23.1) MUTATED            6       10         5         0
  DEL PEAK 36(16Q23.1) WILD-TYPE         47       51        22         2
D63V4, multiclass
            clus
vv           DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            24                            147
  STAGE IIB                             2                              8
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            0                             21
  STAGE IIIB                            8                             70
  STAGE IIIC                            6                             47
  STAGE IV                             10                             51
  STAGE IVA                             5                             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 36(16Q23.1) MUTATED     0  14  55  12
  DEL PEAK 36(16Q23.1) WILD-TYPE  20  91 357  53
D63V5, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  T1                            0                             20
  T2                           14                             91
  T3                           55                            357
  T4                           12                             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 36(16Q23.1) MUTATED    47  16  17
  DEL PEAK 36(16Q23.1) WILD-TYPE 294 132  95
D63V6, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  N0                           47                            294
  N1                           16                            132
  N2                           17                             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 36(16Q23.1) MUTATED    57  11   3   0  10
  DEL PEAK 36(16Q23.1) WILD-TYPE 389  63   7   2  53
D63V7, multiclass
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  M0                            57                            389
  M1                            11                             63
  M1A                            3                              7
  M1B                            0                              2
  MX                            10                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    42  39
  DEL PEAK 36(16Q23.1) WILD-TYPE 241 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     42   39
  DEL PEAK 36(16Q23.1) WILD-TYPE  241  282
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  FEMALE                           42                            241
  MALE                             39                            282
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                     48
  DEL PEAK 36(16Q23.1) WILD-TYPE                  330
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                              10
  DEL PEAK 36(16Q23.1) WILD-TYPE                            49
                                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
D63V9, multiclass
                                clus
vv                               DEL PEAK 36(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                     48
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 36(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      330
  COLON MUCINOUS ADENOCARCINOMA                              49
  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"
D63V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED     1  80
  DEL PEAK 36(16Q23.1) WILD-TYPE   8 515
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED      1   80
  DEL PEAK 36(16Q23.1) WILD-TYPE    8  515
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  NO                             1                              8
  YES                           80                            515
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16Q23.1) MUTATED    56   0   3   4
  DEL PEAK 36(16Q23.1) WILD-TYPE 380   5  33  25
D63V11, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  R0                           56                            380
  R1                            0                              5
  R2                            3                             33
  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                          11    34
  DEL PEAK 36(16Q23.1) WILD-TYPE                        45   258
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 36(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 36(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       258
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 37(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(17P12) MUTATED   277  67
  DEL PEAK 37(17P12) WILD-TYPE 189  42
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         344                          231 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                          67                           42 
$`DEL PEAK 37(17P12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        45.60        15.52        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       24.16        20.61        24.69        23.87        20.28        61.84 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.05         2.01        14.01        50.04        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 
        5.98        37.05        19.00        36.00        85.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       25.02        38.99        36.95        37.02         0.99        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05         2.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       24.00        27.02         7.96        19.00        34.03        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       37.02         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 
        0.95        15.75         0.20         5.52        75.25         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65         5.13        83.80        22.36        65.00        61.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       13.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       17.03        29.03        21.99        14.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        13.05        11.08        10.06        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        7.92        15.12        17.13        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      140.38        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 
       26.47       119.93        35.97       117.07        13.38        11.11 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6298 
       16.31        16.24        33.67         1.28         8.35        23.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       61.87        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       36.72        36.00        26.43        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 
       26.99        17.29         6.64        30.28        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        12.72        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
       46.03        34.03         2.01        50.04         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
        1.02        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-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-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-A023 
        1.02        12.00        31.00        70.03        64.01        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        4.60        10.19         6.05         6.05         6.97        13.97 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98        11.01        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         0.49         2.40 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       16.41        10.78        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 
       31.30        14.86         0.39         0.69         0.53         0.76 
TCGA-F5-6864 TCGA-G5-6235 
        0.46        55.76 

$`DEL PEAK 37(17P12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 
        5.26        46.65        23.38        44.91        13.94        16.04 
TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       36.53        33.53        23.61        22.09        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.08        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       24.92        52.44         9.63         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       63.98        13.02         1.02         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       34.03        29.00        26.01         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       20.98         6.97        54.02         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       11.01         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 
        0.99         1.02        17.98        15.95        14.93        17.03 
TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 
       36.03        31.07        53.00        31.00        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 
       26.01        24.00         2.01        13.05        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P 
        4.01         0.99        34.98        15.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        39.06        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
        0.72         0.76         0.92        27.09        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 
        5.19         6.87        50.37        58.39        32.94        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       49.41         6.77       100.01        11.74         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        22.98        30.08        16.01        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 
       15.02        12.00        14.04        16.04        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        12.03        20.19        20.42 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       17.85         4.50        16.14        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA 
        1.51        12.00        10.26       119.70        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
      135.65         7.76        81.37        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       29.59         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       82.39        74.56        43.07        53.62        51.75        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 
        4.11         2.79        14.76        67.00        24.13        10.39 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3600 
        8.45        10.39         8.02         2.01        12.03         6.05 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
       19.99        29.98         0.99        19.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 
       14.01         0.99        20.98        36.03         9.07        10.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 
       49.97        38.96        61.97         1.45         1.81         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        4.73        60.03        15.02        12.99        12.00        36.00 
TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 
       12.95        32.61        20.55        19.96        15.85         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 
       11.51        13.64        17.46         1.02         0.66         1.12 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                      140.38                       135.65 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                       17.03                        19.04 
[1] "0.1 - 140.4 (17.0)" "0.1 - 135.7 (19.0)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   244 113
  DEL PEAK 37(17P12) WILD-TYPE 194  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    244  113
  DEL PEAK 37(17P12) WILD-TYPE  194   49
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  COLON                         244                          194
  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        52        0       19        87         3
  DEL PEAK 37(17P12) WILD-TYPE      50        1       17        84         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17P12) MUTATED           1        16         16         51
  DEL PEAK 37(17P12) WILD-TYPE         2        10          5         27
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(17P12) MUTATED           41       45        20         2
  DEL PEAK 37(17P12) WILD-TYPE         12       16         7         0
D64V4, multiclass
            clus
vv           DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  STAGE I                            52                           50
  STAGE IA                            0                            1
  STAGE II                           19                           17
  STAGE IIA                          87                           84
  STAGE IIB                           3                            7
  STAGE IIC                           1                            2
  STAGE III                          16                           10
  STAGE IIIA                         16                            5
  STAGE IIIB                         51                           27
  STAGE IIIC                         41                           12
  STAGE IV                           45                           16
  STAGE IVA                          20                            7
  STAGE IVB                           2                            0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 37(17P12) MUTATED     9  60 251  41
  DEL PEAK 37(17P12) WILD-TYPE  11  45 161  24
D64V5, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  T1                          9                           11
  T2                         60                           45
  T3                        251                          161
  T4                         41                           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 37(17P12) MUTATED   177 101  81
  DEL PEAK 37(17P12) WILD-TYPE 164  47  31
D64V6, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  N0                        177                          164
  N1                        101                           47
  N2                         81                           31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 37(17P12) MUTATED   257  56   7   2  35
  DEL PEAK 37(17P12) WILD-TYPE 189  18   3   0  28
D64V7, multiclass
     clus
vv    DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  M0                         257                          189
  M1                          56                           18
  M1A                          7                            3
  M1B                          2                            0
  MX                          35                           28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   165 196
  DEL PEAK 37(17P12) WILD-TYPE 118 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    165  196
  DEL PEAK 37(17P12) WILD-TYPE  118  125
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  FEMALE                        165                          118
  MALE                          196                          125
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                    227
  DEL PEAK 37(17P12) WILD-TYPE                  151
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                              16
  DEL PEAK 37(17P12) WILD-TYPE                            43
                              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
D64V9, multiclass
                                clus
vv                               DEL PEAK 37(17P12) MUTATED
  COLON ADENOCARCINOMA                                  227
  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                            43
  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"
D64V10, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED     7 354
  DEL PEAK 37(17P12) WILD-TYPE   2 241
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED      7  354
  DEL PEAK 37(17P12) WILD-TYPE    2  241
     clus
vv    DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  NO                           7                            2
  YES                        354                          241
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 37(17P12) MUTATED   256   3  26  13
  DEL PEAK 37(17P12) WILD-TYPE 180   2  10  16
D64V11, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  R0                        256                          180
  R1                          3                            2
  R2                         26                           10
  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                          32   175
  DEL PEAK 37(17P12) WILD-TYPE                        24   117
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 37(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                32
  WHITE                                                   175
                                  clus
vv                                 DEL PEAK 37(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  24
  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"

Clustering(65) Variable = DEL PEAK 38(17Q24.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(17Q24.3) MUTATED    70  21
  DEL PEAK 38(17Q24.3) WILD-TYPE 396  88
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            91                            484 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            21                             88 
$`DEL PEAK 38(17Q24.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 
       37.02        43.76        37.05        32.45        31.63        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 
       25.18        24.16        24.03        12.99        21.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 
        6.05         2.01        50.04        37.05        19.00         0.99 
TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3989 
       37.02        31.07        27.02        24.00        26.01         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       34.03        42.02         0.99        32.02        33.04         2.96 
TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D 
       39.98         1.58         1.02         0.20         0.20         5.52 
TCGA-AY-A8YK TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4747 
        6.87        12.10         3.29         0.26        48.20         8.02 
TCGA-CM-4751 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 
       27.02         5.03        15.02        15.02        14.99         7.92 
TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 
       12.49        13.41        11.38        38.20       130.65        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 
      140.38        44.32         7.76       117.07        13.38        13.45 
TCGA-F4-6704 TCGA-F4-6809 TCGA-G4-6295 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC 
        1.55         1.28         8.35        10.98         5.98         1.32 
TCGA-QG-A5YV TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 
       26.99        14.50        15.39        65.98         7.07         1.02 
TCGA-AG-3586 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00H 
        1.02         1.02        32.02        28.04        13.94        25.97 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-DC-6155 
        9.07        12.00        41.00         0.69        10.19        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6881 
       15.02         7.10         5.29        24.13        20.91        16.41 
TCGA-F5-6814 
        0.53 

$`DEL PEAK 38(17Q24.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
       47.05        47.01        15.02        11.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       21.99        16.08        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        15.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.95        15.75        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.01       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
        1.32        15.12        17.85         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
      119.70        24.43        92.75        49.91        13.32         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        35.97        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        11.11        13.64         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        28.21        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       47.15        52.80         4.11        10.52         2.79         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.19         5.49        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       67.00        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       19.10        12.72        37.74        10.39         8.45        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        8.02         2.01        24.00        46.03        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-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        48.03        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        37.02        15.95        36.03         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-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        38.04         0.49         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.99        12.00        36.00        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       126.44        41.36        57.24       129.27 
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-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-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.69         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                         14.50                          18.05 
[1] "0.2 - 140.4 (14.5)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.5"
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    68  25
  DEL PEAK 38(17Q24.3) WILD-TYPE 370 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     68   25
  DEL PEAK 38(17Q24.3) WILD-TYPE  370  137
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON                            68                            370
  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        14        0        5        15         0
  DEL PEAK 38(17Q24.3) WILD-TYPE      88        1       31       156        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         16         67
                                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         38       49        18         1
D65V4, multiclass
            clus
vv           DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  STAGE I                              14                             88
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            15                            156
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            5                             16
  STAGE IIIB                           11                             67
  STAGE IIIC                           15                             38
  STAGE IV                             12                             49
  STAGE IVA                             9                             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 38(17Q24.3) MUTATED     0  18  62  14
  DEL PEAK 38(17Q24.3) WILD-TYPE  20  87 350  51
D65V5, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  T1                            0                             20
  T2                           18                             87
  T3                           62                            350
  T4                           14                             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 38(17Q24.3) MUTATED    38  30  26
  DEL PEAK 38(17Q24.3) WILD-TYPE 303 118  86
D65V6, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  N0                           38                            303
  N1                           30                            118
  N2                           26                             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 38(17Q24.3) MUTATED    59  14   6   1  11
  DEL PEAK 38(17Q24.3) WILD-TYPE 387  60   4   1  52
D65V7, multiclass
     clus
vv    DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  M0                            59                            387
  M1                            14                             60
  M1A                            6                              4
  M1B                            1                              1
  MX                            11                             52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    38  56
  DEL PEAK 38(17Q24.3) WILD-TYPE 245 265
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     38   56
  DEL PEAK 38(17Q24.3) WILD-TYPE  245  265
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  FEMALE                           38                            245
  MALE                             56                            265
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                     58
  DEL PEAK 38(17Q24.3) WILD-TYPE                  320
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                              10
  DEL PEAK 38(17Q24.3) WILD-TYPE                            49
                                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
D65V9, multiclass
                                clus
vv                               DEL PEAK 38(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                     58
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    22
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      320
  COLON MUCINOUS ADENOCARCINOMA                              49
  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"
D65V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED     2  92
  DEL PEAK 38(17Q24.3) WILD-TYPE   7 503
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED      2   92
  DEL PEAK 38(17Q24.3) WILD-TYPE    7  503
     clus
vv    DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  NO                             2                              7
  YES                           92                            503
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(17Q24.3) MUTATED    63   0   8   6
  DEL PEAK 38(17Q24.3) WILD-TYPE 373   5  28  23
D65V11, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  R0                           63                            373
  R1                            0                              5
  R2                            8                             28
  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                           9    45
  DEL PEAK 38(17Q24.3) WILD-TYPE                        47   247
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 38(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 38(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    47
  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"

Clustering(66) Variable = DEL PEAK 39(18P11.31) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 39(18P11.31) MUTATED   286  62
  DEL PEAK 39(18P11.31) WILD-TYPE 180  47
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            348                             227 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                             62                              47 
$`DEL PEAK 39(18P11.31) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        24.13        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 
        6.97        38.99         9.07        37.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       34.03        29.00        26.01        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       24.00        23.01        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       18.05        12.99        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
        7.96        13.94        19.00        34.03        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        14.99        21.99        15.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       31.00         1.02        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 
        2.01         5.03        41.00        40.96         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        1.58         1.02         0.10         0.20         0.43        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
        0.95        15.75         5.19         5.52         6.87        75.25 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         1.94         2.24         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 
        3.29         0.07         0.26         1.35        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        2.01         8.02         8.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       16.04        21.99        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       11.51        20.19        18.25         1.32        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
       12.49         7.53        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.38        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      140.38        44.32       139.17        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 
      117.07        95.18        13.38        11.11        13.45         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       35.41        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       55.04        45.11        36.72        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 
       47.15         4.11        10.98        10.52         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 
        5.49        26.99        17.29         6.64        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       10.39        14.50        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       36.03         7.07         1.02         2.01        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       34.03        50.04         0.99        15.95        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        36.03         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
       13.94         6.02        25.97        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        70.03        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
        7.10        30.05        12.95        13.05        10.06       126.44 
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-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76         0.46        18.28        55.76 

$`DEL PEAK 39(18P11.31) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 
       46.65        23.38        16.04        31.63        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.52         8.38        24.16        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        24.03        36.03         8.05 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       29.00        12.99         0.99        21.01        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       20.98        61.02         6.97        54.02         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       36.03        32.05        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       33.01        26.01        24.00         2.01         2.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       27.02        19.07        27.02        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01         0.99        17.03        34.98         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07        21.37        56.55         0.72         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 
       17.82        50.37        58.39         1.41        32.94        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       49.41         6.77       100.01        11.74         3.19         3.06 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       23.05        20.02        37.02        26.04        27.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       16.01        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 
       12.99        14.04        12.95        13.05        11.08        19.59 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75         7.92        15.12         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       15.58        12.39        10.13         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        49.91         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      131.51       135.65         7.76         6.12        14.04        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24         8.61        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        43.07        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       51.75        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        35.80        26.17        52.80         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 
        5.59        14.76        67.00        19.10         8.45        15.39 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3594 
       10.39        12.00        32.02         8.02         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3892 
       12.03         6.05        19.99         0.99         0.99        13.02 
TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01Y 
       14.01        14.04        20.98        23.01        36.03        64.01 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
       49.97        38.96        61.97         1.45         1.81         5.29 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       32.61        19.96        20.91         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 TCGA-G5-6641 
        9.96         0.53         1.12        47.08        26.43 

  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                         140.38                          135.65 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                          17.03                           19.04 
[1] "0.1 - 140.4 (17.0)" "0.1 - 135.7 (19.0)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   238 122
  DEL PEAK 39(18P11.31) WILD-TYPE 200  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    238  122
  DEL PEAK 39(18P11.31) WILD-TYPE  200   40
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  COLON                            238                             200
  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        56        0       14        96         4
  DEL PEAK 39(18P11.31) WILD-TYPE      46        1       22        75         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18P11.31) MUTATED           3        12         13         51
  DEL PEAK 39(18P11.31) WILD-TYPE         0        14          8         27
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(18P11.31) MUTATED           34       47        24         1
  DEL PEAK 39(18P11.31) WILD-TYPE         19       14         3         1
D66V4, multiclass
            clus
vv           DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  STAGE I                               56                              46
  STAGE IA                               0                               1
  STAGE II                              14                              22
  STAGE IIA                             96                              75
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             12                              14
  STAGE IIIA                            13                               8
  STAGE IIIB                            51                              27
  STAGE IIIC                            34                              19
  STAGE IV                              47                              14
  STAGE IVA                             24                               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 39(18P11.31) MUTATED    11  61 251  40
  DEL PEAK 39(18P11.31) WILD-TYPE   9  44 161  25
D66V5, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  T1                            11                               9
  T2                            61                              44
  T3                           251                             161
  T4                            40                              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 39(18P11.31) MUTATED   187 102  72
  DEL PEAK 39(18P11.31) WILD-TYPE 154  46  40
D66V6, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  N0                           187                             154
  N1                           102                              46
  N2                            72                              40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 39(18P11.31) MUTATED   253  60  10   1  35
  DEL PEAK 39(18P11.31) WILD-TYPE 193  14   0   1  28
D66V7, multiclass
     clus
vv    DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  M0                            253                             193
  M1                             60                              14
  M1A                            10                               0
  M1B                             1                               1
  MX                             35                              28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   168 195
  DEL PEAK 39(18P11.31) WILD-TYPE 115 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    168  195
  DEL PEAK 39(18P11.31) WILD-TYPE  115  126
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  FEMALE                           168                             115
  MALE                             195                             126
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                    227
  DEL PEAK 39(18P11.31) WILD-TYPE                  151
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                              10
  DEL PEAK 39(18P11.31) WILD-TYPE                            49
                                 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
D66V9, multiclass
                                clus
vv                               DEL PEAK 39(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                     227
  COLON MUCINOUS ADENOCARCINOMA                             10
  RECTAL ADENOCARCINOMA                                    116
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 39(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       151
  COLON MUCINOUS ADENOCARCINOMA                               49
  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"
D66V10, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED     7 356
  DEL PEAK 39(18P11.31) WILD-TYPE   2 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED      7  356
  DEL PEAK 39(18P11.31) WILD-TYPE    2  239
     clus
vv    DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  NO                              7                               2
  YES                           356                             239
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 39(18P11.31) MUTATED   259   2  29  14
  DEL PEAK 39(18P11.31) WILD-TYPE 177   3   7  15
D66V11, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  R0                           259                             177
  R1                             2                               3
  R2                            29                               7
  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                          36   180
  DEL PEAK 39(18P11.31) WILD-TYPE                        20   112
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 39(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      180
                                  clus
vv                                 DEL PEAK 39(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DEL PEAK 40(18Q12.2) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(18Q12.2) MUTATED   317  73
  DEL PEAK 40(18Q12.2) WILD-TYPE 149  36
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           390                            185 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                            73                             36 
$`DEL PEAK 40(18Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        6.97        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       18.05        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02         0.99        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        0.92        41.00        40.96         4.21         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31        15.75         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
       61.41        12.10        29.56         5.23         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25         1.32        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        11.11        13.45 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       35.41        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        91.79        46.75        47.15         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       10.52         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        6.64        30.28        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        12.72        37.74        10.39        14.50 
TCGA-AF-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         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       24.00        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 40(18Q12.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       46.65        23.38        33.53        22.09        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 
        1.02        13.02         1.02         8.05        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       47.05        11.01         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        32.05        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       26.01        24.00         2.01        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       27.02         0.99        34.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R 
        1.02        35.01        35.01        39.06        51.98        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       39.98        18.05         0.07        21.37        56.55         0.72 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95         0.20        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 
       50.37        58.39         1.41         5.65        32.94        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         3.19         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       13.05        20.42        17.75         7.92        15.12         4.50 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       16.14        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F 
       10.26       119.70       135.65         7.76        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 
       60.79        98.24        13.64         6.18        35.87        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       19.43       107.67        74.56        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 
       52.80         2.79         5.98         5.59        14.76        67.00 
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
        8.45         8.02         1.02        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A025 
       13.02        14.01        20.98        36.03         9.07        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                         17.08                          19.04 
[1] "0.1 - 140.4 (17.1)" "0.1 - 135.7 (19.0)"
[1] "hr=" "1"  
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   266 139
  DEL PEAK 40(18Q12.2) WILD-TYPE 172  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    266  139
  DEL PEAK 40(18Q12.2) WILD-TYPE  172   23
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON                           266                            172
  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        59        0       21       105         4
  DEL PEAK 40(18Q12.2) WILD-TYPE      43        1       15        66         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q12.2) MUTATED           3        15         17         58
  DEL PEAK 40(18Q12.2) WILD-TYPE         0        11          4         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18Q12.2) MUTATED           40       52        23         1
  DEL PEAK 40(18Q12.2) WILD-TYPE         13        9         4         1
D67V4, multiclass
            clus
vv           DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  STAGE I                              59                             43
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                           105                             66
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            15                             11
  STAGE IIIA                           17                              4
  STAGE IIIB                           58                             20
  STAGE IIIC                           40                             13
  STAGE IV                             52                              9
  STAGE IVA                            23                              4
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 40(18Q12.2) MUTATED    11  67 287  42
  DEL PEAK 40(18Q12.2) WILD-TYPE   9  38 125  23
D67V5, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  T1                           11                              9
  T2                           67                             38
  T3                          287                            125
  T4                           42                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 40(18Q12.2) MUTATED   205 114  86
  DEL PEAK 40(18Q12.2) WILD-TYPE 136  34  26
D67V6, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  N0                          205                            136
  N1                          114                             34
  N2                           86                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 40(18Q12.2) MUTATED   291  63   9   1  39
  DEL PEAK 40(18Q12.2) WILD-TYPE 155  11   1   1  24
D67V7, multiclass
     clus
vv    DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  M0                           291                            155
  M1                            63                             11
  M1A                            9                              1
  M1B                            1                              1
  MX                            39                             24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   185 223
  DEL PEAK 40(18Q12.2) WILD-TYPE  98  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    185  223
  DEL PEAK 40(18Q12.2) WILD-TYPE   98   98
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  FEMALE                          185                             98
  MALE                            223                             98
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                    250
  DEL PEAK 40(18Q12.2) WILD-TYPE                  128
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                              15
  DEL PEAK 40(18Q12.2) WILD-TYPE                            44
                                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
D67V9, multiclass
                                clus
vv                               DEL PEAK 40(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    250
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                   128
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  COLON MUCINOUS ADENOCARCINOMA                              44
  RECTAL ADENOCARCINOMA                                      18
  RECTAL MUCINOUS ADENOCARCINOMA                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED     9 399
  DEL PEAK 40(18Q12.2) WILD-TYPE   0 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED      9  399
  DEL PEAK 40(18Q12.2) WILD-TYPE    0  196
     clus
vv    DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  NO                             9                              0
  YES                          399                            196
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(18Q12.2) MUTATED   292   3  29  14
  DEL PEAK 40(18Q12.2) WILD-TYPE 144   2   7  15
D67V11, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  R0                          292                            144
  R1                            3                              2
  R2                           29                              7
  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                          36   203
  DEL PEAK 40(18Q12.2) WILD-TYPE                        20    89
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     203
                                  clus
vv                                 DEL PEAK 40(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    20
  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"

Clustering(68) Variable = DEL PEAK 41(18Q21.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q21.2) MUTATED   331  76
  DEL PEAK 41(18Q21.2) WILD-TYPE 135  33
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           407                            168 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                            76                             33 
$`DEL PEAK 41(18Q21.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.39        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        52.44         9.63         5.03         1.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       37.05         1.02         6.97        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03        19.07        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        25.02        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        19.00        34.03        18.05        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6386 
        0.43         0.46        14.50        16.31        15.75        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
        5.19         5.52         6.87        75.25         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       11.51        20.19        17.75        18.25         1.32        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       26.47       119.93        35.97       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        11.11        13.45         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.04        91.79        46.75        47.15         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        10.52         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       26.99        17.29         6.64        30.28        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39        14.50        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        36.95        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-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        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       14.86         0.39         1.02         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 41(18Q21.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       46.65        23.38        33.53        22.06         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
        1.02         8.05        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       20.98         6.97         0.92        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        1.02        17.98        15.95        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        17.03         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       39.06        51.98        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       21.37        56.55         0.72         0.76         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        21.44        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 
       32.94        49.41         6.77       100.01         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       20.42         7.92        15.12         4.50        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 
      135.65         7.76        81.37        60.79        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       35.87        19.43       107.67        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       26.43        22.09        13.78        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3580 
        2.79         5.59        14.76        67.00         8.45         8.02 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       12.03        19.99         0.99        13.02        14.01        20.98 
TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-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                           0.07 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        17.230                         19.055 
[1] "0.1 - 140.4 (17.2)" "0.1 - 135.7 (19.1)"
[1] "hr=" "1"  
D68V2, continuous
D68V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   280 142
  DEL PEAK 41(18Q21.2) WILD-TYPE 158  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    280  142
  DEL PEAK 41(18Q21.2) WILD-TYPE  158   20
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON                           280                            158
  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        61        0       23       107         4
  DEL PEAK 41(18Q21.2) WILD-TYPE      41        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q21.2) MUTATED           3        16         17         61
  DEL PEAK 41(18Q21.2) WILD-TYPE         0        10          4         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(18Q21.2) MUTATED           43       55        24         2
  DEL PEAK 41(18Q21.2) WILD-TYPE         10        6         3         0
D68V4, multiclass
            clus
vv           DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  STAGE I                              61                             41
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           107                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           17                              4
  STAGE IIIB                           61                             17
  STAGE IIIC                           43                             10
  STAGE IV                             55                              6
  STAGE IVA                            24                              3
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 41(18Q21.2) MUTATED    12  68 298  46
  DEL PEAK 41(18Q21.2) WILD-TYPE   8  37 114  19
D68V5, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  T1                           12                              8
  T2                           68                             37
  T3                          298                            114
  T4                           46                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 41(18Q21.2) MUTATED   211 118  93
  DEL PEAK 41(18Q21.2) WILD-TYPE 130  30  19
D68V6, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  N0                          211                            130
  N1                          118                             30
  N2                           93                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 41(18Q21.2) MUTATED   301  67   9   2  42
  DEL PEAK 41(18Q21.2) WILD-TYPE 145   7   1   0  21
D68V7, multiclass
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  M0                           301                            145
  M1                            67                              7
  M1A                            9                              1
  M1B                            2                              0
  MX                            42                             21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   190 235
  DEL PEAK 41(18Q21.2) WILD-TYPE  93  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    190  235
  DEL PEAK 41(18Q21.2) WILD-TYPE   93   86
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  FEMALE                          190                             93
  MALE                            235                             86
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                    262
  DEL PEAK 41(18Q21.2) WILD-TYPE                  116
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                              17
  DEL PEAK 41(18Q21.2) WILD-TYPE                            42
                                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
D68V9, multiclass
                                clus
vv                               DEL PEAK 41(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                    262
  COLON MUCINOUS ADENOCARCINOMA                            17
  RECTAL ADENOCARCINOMA                                   129
  RECTAL MUCINOUS ADENOCARCINOMA                           11
                                clus
vv                               DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      116
  COLON MUCINOUS ADENOCARCINOMA                              42
  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"
D68V10, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED     9 416
  DEL PEAK 41(18Q21.2) WILD-TYPE   0 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED      9  416
  DEL PEAK 41(18Q21.2) WILD-TYPE    0  179
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  NO                             9                              0
  YES                          416                            179
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(18Q21.2) MUTATED   302   3  30  15
  DEL PEAK 41(18Q21.2) WILD-TYPE 134   2   6  14
D68V11, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  R0                          302                            134
  R1                            3                              2
  R2                           30                              6
  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                          40   212
  DEL PEAK 41(18Q21.2) WILD-TYPE                        16    80
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  40
  WHITE                                                     212
                                  clus
vv                                 DEL PEAK 41(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  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"

Clustering(69) Variable = DEL PEAK 42(18Q22.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q22.1) MUTATED   327  76
  DEL PEAK 42(18Q22.1) WILD-TYPE 139  33
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           403                            172 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                            76                             33 
$`DEL PEAK 42(18Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.39        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        52.44         9.63         5.03         1.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       37.05         1.02         6.97        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03        19.07        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        25.02        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        33.07         0.99        31.07        31.07 
TCGA-AA-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-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       12.99        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       27.02         7.96        13.94        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       32.02        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96         4.21         0.79         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
        0.20         0.43         0.46        14.50        16.31        15.75 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
        5.19         5.52         6.87        75.25         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 
        2.14         3.29         0.07         0.26         1.35        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       21.99         2.01         8.02         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.19        17.75        18.25         1.32        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       26.47       119.93        35.97       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        11.11        13.45         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        91.79        46.75        47.15         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.52         5.98         1.32         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       17.29         6.64        30.28        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-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         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-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 
        0.49         0.69         0.72         4.60        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       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 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 42(18Q22.1) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       46.65        23.38        33.53        22.06         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
        1.02         8.05        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       20.98         6.97         0.92        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3877 
        1.02        17.98        15.95        36.03        32.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       19.07        27.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       17.03         4.01        27.02         0.99        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       31.00        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       51.98        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.72         0.76         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        21.44        17.82        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 
       32.94        49.41         6.77       100.01         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        26.04        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       12.95        20.42         7.92         4.50        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 
      135.65         7.76        81.37        60.79        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       35.87        19.43       107.67        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 
       52.80         2.79         5.59        14.76        67.00         8.45 
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         1.02         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                           0.07 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                        17.130                         18.545 
[1] "0.1 - 140.4 (17.1)" "0.1 - 135.7 (18.5)"
[1] "hr=" "1"  
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   279 138
  DEL PEAK 42(18Q22.1) WILD-TYPE 159  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    279  138
  DEL PEAK 42(18Q22.1) WILD-TYPE  159   24
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON                           279                            159
  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        61        0       23       107         4
  DEL PEAK 42(18Q22.1) WILD-TYPE      41        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q22.1) MUTATED           3        14         16         60
  DEL PEAK 42(18Q22.1) WILD-TYPE         0        12          5         18
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(18Q22.1) MUTATED           43       54        24         2
  DEL PEAK 42(18Q22.1) WILD-TYPE         10        7         3         0
D69V4, multiclass
            clus
vv           DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  STAGE I                              61                             41
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           107                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            14                             12
  STAGE IIIA                           16                              5
  STAGE IIIB                           60                             18
  STAGE IIIC                           43                             10
  STAGE IV                             54                              7
  STAGE IVA                            24                              3
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(18Q22.1) MUTATED    12  68 293  46
  DEL PEAK 42(18Q22.1) WILD-TYPE   8  37 119  19
D69V5, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  T1                           12                              8
  T2                           68                             37
  T3                          293                            119
  T4                           46                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 42(18Q22.1) MUTATED   211 114  92
  DEL PEAK 42(18Q22.1) WILD-TYPE 130  34  20
D69V6, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  N0                          211                            130
  N1                          114                             34
  N2                           92                             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 42(18Q22.1) MUTATED   298  66   9   2  41
  DEL PEAK 42(18Q22.1) WILD-TYPE 148   8   1   0  22
D69V7, multiclass
     clus
vv    DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  M0                           298                            148
  M1                            66                              8
  M1A                            9                              1
  M1B                            2                              0
  MX                            41                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   188 232
  DEL PEAK 42(18Q22.1) WILD-TYPE  95  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    188  232
  DEL PEAK 42(18Q22.1) WILD-TYPE   95   89
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  FEMALE                          188                             95
  MALE                            232                             89
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                    262
  DEL PEAK 42(18Q22.1) WILD-TYPE                  116
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                              16
  DEL PEAK 42(18Q22.1) WILD-TYPE                            43
                                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
D69V9, multiclass
                                clus
vv                               DEL PEAK 42(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    262
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                   127
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      116
  COLON MUCINOUS ADENOCARCINOMA                              43
  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"
D69V10, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED     9 411
  DEL PEAK 42(18Q22.1) WILD-TYPE   0 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED      9  411
  DEL PEAK 42(18Q22.1) WILD-TYPE    0  184
     clus
vv    DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  NO                             9                              0
  YES                          411                            184
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q22.1) MUTATED   299   3  29  15
  DEL PEAK 42(18Q22.1) WILD-TYPE 137   2   7  14
D69V11, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  R0                          299                            137
  R1                            3                              2
  R2                           29                              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"
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                          39   210
  DEL PEAK 42(18Q22.1) WILD-TYPE                        17    82
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     210
                                  clus
vv                                 DEL PEAK 42(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                        82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = DEL PEAK 43(19P13.3) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(19P13.3) MUTATED    66  22
  DEL PEAK 43(19P13.3) WILD-TYPE 400  87
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            88                            487 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            22                             87 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3519 
       34.65        25.08        21.76        61.84        58.03         9.07 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       26.01        12.99        13.02        23.01        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3860 TCGA-AA-3866 
        2.01        36.00        36.95        37.02        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 
       24.03        27.02        24.00         2.01        50.99        24.00 
TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F 
       27.02         0.99        12.00        33.04        26.01        39.98 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4616 
       41.00         1.02         0.20        16.31         0.20         5.13 
TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6169 TCGA-CM-6675 
       65.00         3.29       102.44        48.20        13.02        13.05 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6541 
       10.06        14.99        20.19         1.32         4.50        15.58 
TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-F4-6461 TCGA-F4-6808 
       10.13       119.70        44.32       131.51        11.11        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL TCGA-AF-2687 
        8.35        82.39        36.00        10.98        30.28        24.13 
TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 TCGA-AG-3732 
       17.95        14.50        12.00         1.02        15.95        32.98 
TCGA-AG-3893 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6619 
       35.01        17.03        15.95         9.07        64.01         6.05 
TCGA-CI-6620 TCGA-CL-4957 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 
        6.05        13.97        12.99        13.97         7.10         5.29 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 
      129.27        24.13        51.48        17.00        16.34        13.64 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 
       31.30        14.86         0.39        18.28 

$`DEL PEAK 43(19P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       21.01        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       53.00        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         1.58         0.10 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.03        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         7.92        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14         7.53        12.39        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        6.64        14.76        67.00        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        37.74        10.39         8.45        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-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        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-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        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-4022 
       19.99        28.04        36.03        14.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       36.03         1.02        12.00        31.00        70.03        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-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        1.81        10.19         6.97         9.37         4.73        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
        7.99        10.98        11.01        15.02        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       36.00        30.05        12.95        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       41.36        57.24        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        37.51         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                         17.03                          17.85 
[1] "0.2 - 131.5 (17.0)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.3"
D70V2, continuous
D70V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    61  33
  DEL PEAK 43(19P13.3) WILD-TYPE 377 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     61   33
  DEL PEAK 43(19P13.3) WILD-TYPE  377  129
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  COLON                            61                            377
  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      91        1       32       152        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(19P13.3) MUTATED           1         5          5          9
  DEL PEAK 43(19P13.3) WILD-TYPE         2        21         16         69
                                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         38       46        19         1
D70V4, multiclass
            clus
vv           DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                              11                             91
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            19                            152
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             5                             21
  STAGE IIIA                            5                             16
  STAGE IIIB                            9                             69
  STAGE IIIC                           15                             38
  STAGE IV                             15                             46
  STAGE IVA                             8                             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 43(19P13.3) MUTATED     1  13  71  10
  DEL PEAK 43(19P13.3) WILD-TYPE  19  92 341  55
D70V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T1                            1                             19
  T2                           13                             92
  T3                           71                            341
  T4                           10                             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 43(19P13.3) MUTATED    37  27  31
  DEL PEAK 43(19P13.3) WILD-TYPE 304 121  81
D70V6, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           37                            304
  N1                           27                            121
  N2                           31                             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 43(19P13.3) MUTATED    62  19   3   1   9
  DEL PEAK 43(19P13.3) WILD-TYPE 384  55   7   1  54
D70V7, multiclass
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  M0                            62                            384
  M1                            19                             55
  M1A                            3                              7
  M1B                            1                              1
  MX                             9                             54
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    40  55
  DEL PEAK 43(19P13.3) WILD-TYPE 243 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     40   55
  DEL PEAK 43(19P13.3) WILD-TYPE  243  266
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           40                            243
  MALE                             55                            266
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                     55
  DEL PEAK 43(19P13.3) WILD-TYPE                  323
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                               5
  DEL PEAK 43(19P13.3) WILD-TYPE                            54
                                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
D70V9, multiclass
                                clus
vv                               DEL PEAK 43(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                     55
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 43(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      323
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                     115
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED     2  93
  DEL PEAK 43(19P13.3) WILD-TYPE   7 502
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED      2   93
  DEL PEAK 43(19P13.3) WILD-TYPE    7  502
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                             2                              7
  YES                           93                            502
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(19P13.3) MUTATED    62   1  10   4
  DEL PEAK 43(19P13.3) WILD-TYPE 374   4  26  25
D70V11, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  R0                           62                            374
  R1                            1                              4
  R2                           10                             26
  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                           7    42
  DEL PEAK 43(19P13.3) WILD-TYPE                        49   250
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    49
  WHITE                                                       250
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = DEL PEAK 44(20P12.1) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(20P12.1) MUTATED   101  28
  DEL PEAK 44(20P12.1) WILD-TYPE 365  81
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           129                            446 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                            28                             81 
$`DEL PEAK 44(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       17.79        14.53        29.19        23.61        32.71        29.16 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3519 
       24.13        25.18        21.76         1.02        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3561 
       34.03        26.01        12.99         0.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3855 
       78.08         5.98        85.05        25.02        36.95        32.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
       24.03         2.01        20.98         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F 
       42.02        32.02        31.00         1.02        37.02        39.98 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 
       40.96         0.20        15.75        75.25        62.79         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 
       11.74         1.94       102.44        21.99         2.01        22.03 
TCGA-CM-5349 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       30.08        29.03        12.99        13.02        15.02        11.08 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6929 TCGA-D5-6932 
       13.51        11.51         1.32         7.92        13.41        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28E TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      131.51        26.47       119.93        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 TCGA-G4-6320 
        1.28         0.53         8.35        23.51        36.72        26.43 
TCGA-NH-A50V TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-3913 
       10.52         5.49         6.64        30.28        17.95        10.39 
TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 
       14.50        86.63        65.98        11.84        36.03        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3742 
        7.07         2.01        24.00         6.05        15.95         0.99 
TCGA-AG-3883 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L 
        1.02        32.02         0.99        13.94         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6547 
       31.00        70.03        64.01         1.94        38.96         1.45 
TCGA-AH-6643 TCGA-CI-6624 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 
        0.69         4.73        12.00         7.10        30.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       41.36        57.24        24.13        32.61         2.40        15.85 
TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.41        11.51        10.78         8.45        31.30 
TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       14.86         0.46        26.43 

$`DEL PEAK 44(20P12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       32.45        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.06        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         1.02         3.02         1.02        37.05        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        29.00        14.01        33.99        21.01        13.02 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 
       12.99        24.00        33.01        26.01        24.00        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       22.03        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52         6.87        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        48.20        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        16.04        21.99        14.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       10.06        12.03        14.99        12.26        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1D9 
        1.51        12.00        10.26        24.43        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        81.37        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 
        6.18        35.87         1.55        16.31        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        82.39        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98         2.79         5.98         5.59         1.32         5.19 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       26.99        17.29        14.76        67.00        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       43.04        13.55        19.10        12.72        37.74         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 
       15.39        20.02        10.39        12.00         8.02         1.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-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-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
        1.02        32.98         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         0.49         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02        36.00        12.95        13.05         5.29       126.44 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 
       17.00        18.28        16.34        16.31         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       17.46        11.97         9.96        37.51         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                        17.950                         17.785 
[1] "0.2 - 131.5 (17.9)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D71V2, continuous
D71V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    83  48
  DEL PEAK 44(20P12.1) WILD-TYPE 355 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     83   48
  DEL PEAK 44(20P12.1) WILD-TYPE  355  114
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  COLON                            83                            355
  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        31         0
  DEL PEAK 44(20P12.1) WILD-TYPE      85        1       25       140        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(20P12.1) MUTATED           2         4          6         21
  DEL PEAK 44(20P12.1) WILD-TYPE         1        22         15         57
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(20P12.1) MUTATED           16       14         8         0
  DEL PEAK 44(20P12.1) WILD-TYPE         37       47        19         2
D71V4, multiclass
            clus
vv           DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  STAGE I                              17                             85
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            31                            140
  STAGE IIB                             0                             10
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            6                             15
  STAGE IIIB                           21                             57
  STAGE IIIC                           16                             37
  STAGE IV                             14                             47
  STAGE IVA                             8                             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 44(20P12.1) MUTATED     3  20  95  14
  DEL PEAK 44(20P12.1) WILD-TYPE  17  85 317  51
D71V5, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  T1                            3                             17
  T2                           20                             85
  T3                           95                            317
  T4                           14                             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 44(20P12.1) MUTATED    66  36  30
  DEL PEAK 44(20P12.1) WILD-TYPE 275 112  82
D71V6, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  N0                           66                            275
  N1                           36                            112
  N2                           30                             82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 44(20P12.1) MUTATED   100  19   1   0  12
  DEL PEAK 44(20P12.1) WILD-TYPE 346  55   9   2  51
D71V7, multiclass
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  M0                           100                            346
  M1                            19                             55
  M1A                            1                              9
  M1B                            0                              2
  MX                            12                             51
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    65  67
  DEL PEAK 44(20P12.1) WILD-TYPE 218 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     65   67
  DEL PEAK 44(20P12.1) WILD-TYPE  218  254
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  FEMALE                           65                            218
  MALE                             67                            254
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                     77
  DEL PEAK 44(20P12.1) WILD-TYPE                  301
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                               6
  DEL PEAK 44(20P12.1) WILD-TYPE                            53
                                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
D71V9, multiclass
                                clus
vv                               DEL PEAK 44(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                     77
  COLON MUCINOUS ADENOCARCINOMA                             6
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 44(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      301
  COLON MUCINOUS ADENOCARCINOMA                              53
  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"
D71V10, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED     0 132
  DEL PEAK 44(20P12.1) WILD-TYPE   9 463
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED      0  132
  DEL PEAK 44(20P12.1) WILD-TYPE    9  463
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  NO                             0                              9
  YES                          132                            463
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(20P12.1) MUTATED    91   1   8   3
  DEL PEAK 44(20P12.1) WILD-TYPE 345   4  28  26
D71V11, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  R0                           91                            345
  R1                            1                              4
  R2                            8                             28
  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                          13    69
  DEL PEAK 44(20P12.1) WILD-TYPE                        43   223
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 44(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      69
                                  clus
vv                                 DEL PEAK 44(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    43
  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"

Clustering(72) Variable = DEL PEAK 45(21Q11.2) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q11.2) MUTATED   160  39
  DEL PEAK 45(21Q11.2) WILD-TYPE 306  70
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           199                            376 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                            39                             70 
$`DEL PEAK 45(21Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 
       37.02        43.76        42.28        37.05        14.53        30.44 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 
       38.99         9.07        19.07        19.07        34.03        26.01 
TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3685 
       14.01        13.02        23.01        19.99        78.08        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       19.00        36.00         0.99        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       18.05        24.00        20.98         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C 
       13.94        17.03        27.02        42.02        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        0.99        32.02        31.00        51.98        39.98         2.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
        0.92        41.00         0.79         1.02         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 
       14.50        16.31         0.95         5.52         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         3.19         2.24         2.14 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
        3.29         0.26        48.20        21.99         2.01        20.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        8.02        27.02        13.02        22.03        16.01         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        29.03        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       14.99        17.75         1.32        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
        9.04        13.41        11.38        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        7.50       131.51        26.47        13.38        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       29.59        16.24        33.67         0.53        35.41         8.35 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.72        36.00        26.43        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 
        4.11         5.98         5.19        26.99        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       17.23        19.10        14.50        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       86.63        11.84        36.03        12.00         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3728 
       24.00        46.03        34.03        12.03        19.99        29.98 
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         0.49 
TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 
        0.69         4.73        13.97        10.98        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG 
        7.10        13.05        10.06       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         1.02         0.66         0.53         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 45(21Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        15.52        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        33.53        23.61        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 
       20.12        19.66        16.24        24.92        52.44         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       36.03         8.05        29.00        29.00        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       15.02        11.01         5.98         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       17.98        15.95        36.95        17.03        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       12.99        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98        15.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R 
       26.01        37.02        39.06         2.96         5.03        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.72         1.58         0.10         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 
       49.41         6.77       100.01        11.74         1.94         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
        2.93       124.27        23.05        37.02         8.02        26.04 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.98        30.08        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        18.25         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.39         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        92.75        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31         1.28        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 
       55.04        51.75        45.11        39.42        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U 
       13.78        35.80        26.17        47.15        52.80        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX 
       10.52         2.79         5.59         1.32         5.49        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
        6.64        14.76        30.28        67.00        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3578 
       12.72        37.74        10.39         8.45        65.98        32.02 
TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
        8.02         2.01         1.02         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         0.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       35.01        14.01        32.02        28.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-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         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       11.01        15.02        12.99        12.00        15.02        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6507 
       12.95         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        37.51        14.86         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.46        55.76        47.08 

  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        17.030                         18.015 
[1] "0.2 - 140.4 (17.0)" "0.1 - 139.2 (18.0)"
[1] "hr=" "1.2"
D72V2, continuous
D72V3, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   135  71
  DEL PEAK 45(21Q11.2) WILD-TYPE 303  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    135   71
  DEL PEAK 45(21Q11.2) WILD-TYPE  303   91
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON                           135                            303
  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        33        0       14        53         2
  DEL PEAK 45(21Q11.2) WILD-TYPE      69        1       22       118         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(21Q11.2) MUTATED           1         7         11         27
  DEL PEAK 45(21Q11.2) WILD-TYPE         2        19         10         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 45(21Q11.2) MUTATED           21       28         7         0
  DEL PEAK 45(21Q11.2) WILD-TYPE         32       33        20         2
D72V4, multiclass
            clus
vv           DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  STAGE I                              33                             69
  STAGE IA                              0                              1
  STAGE II                             14                             22
  STAGE IIA                            53                            118
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                           11                             10
  STAGE IIIB                           27                             51
  STAGE IIIC                           21                             32
  STAGE IV                             28                             33
  STAGE IVA                             7                             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 45(21Q11.2) MUTATED     7  39 140  23
  DEL PEAK 45(21Q11.2) WILD-TYPE  13  66 272  42
D72V5, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  T1                            7                             13
  T2                           39                             66
  T3                          140                            272
  T4                           23                             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 45(21Q11.2) MUTATED   106  56  47
  DEL PEAK 45(21Q11.2) WILD-TYPE 235  92  65
D72V6, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  N0                          106                            235
  N1                           56                             92
  N2                           47                             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 45(21Q11.2) MUTATED   149  30   3   0  26
  DEL PEAK 45(21Q11.2) WILD-TYPE 297  44   7   2  37
D72V7, multiclass
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  M0                           149                            297
  M1                            30                             44
  M1A                            3                              7
  M1B                            0                              2
  MX                            26                             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    95 114
  DEL PEAK 45(21Q11.2) WILD-TYPE 188 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     95  114
  DEL PEAK 45(21Q11.2) WILD-TYPE  188  207
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  FEMALE                           95                            188
  MALE                            114                            207
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                    126
  DEL PEAK 45(21Q11.2) WILD-TYPE                  252
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                               8
  DEL PEAK 45(21Q11.2) WILD-TYPE                            51
                                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
D72V9, multiclass
                                clus
vv                               DEL PEAK 45(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    126
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      252
  COLON MUCINOUS ADENOCARCINOMA                              51
  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"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED     5 204
  DEL PEAK 45(21Q11.2) WILD-TYPE   4 391
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED      5  204
  DEL PEAK 45(21Q11.2) WILD-TYPE    4  391
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  NO                             5                              4
  YES                          204                            391
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(21Q11.2) MUTATED   148   2  14   7
  DEL PEAK 45(21Q11.2) WILD-TYPE 288   3  22  22
D72V11, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  R0                          148                            288
  R1                            2                              3
  R2                           14                             22
  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                          17   105
  DEL PEAK 45(21Q11.2) WILD-TYPE                        39   187
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                     105
                                  clus
vv                                 DEL PEAK 45(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       187
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = DEL PEAK 46(22Q13.32) MUTATION ANALYSIS
D73V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(22Q13.32) MUTATED   163  46
  DEL PEAK 46(22Q13.32) WILD-TYPE 303  63
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            209                             366 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                             46                              63 
$`DEL PEAK 46(22Q13.32) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       15.52        34.65        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       29.19        23.61        22.52        20.61        21.76        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         9.63         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       24.03        37.05        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 
       21.01        13.02        19.99        13.94         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 
       50.04         5.98        37.05        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 
       29.98        18.05         2.01        12.99         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 
       21.99        50.99        13.05        26.01         7.96        13.94 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W 
       15.02        33.04        26.01        37.02        39.98        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       40.96         1.58         1.02         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 TCGA-AZ-4614 
       16.31        15.75         0.20         5.52         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6748 
        2.24         3.06         0.26         1.35        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
        8.02         8.02        29.06        30.08         5.03        15.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        14.99        13.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.19         1.32         7.92        15.12        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 
        7.53        12.43        13.41        11.38       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       12.59       140.38        44.32       131.51         6.12        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 
       13.38         1.55        16.24         1.28         8.35        82.39 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       51.75        45.11        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL 
        4.11        10.98        10.52         5.98        26.99        30.28 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
       13.55        19.10        14.50        15.39        10.39        65.98 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07         1.02         2.01        24.00 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 
       34.03        50.04        15.95        29.98         1.02        19.99 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02         1.02        19.99        28.04        36.03        14.04 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       25.97        23.01        12.00        10.98         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 
       41.00         0.49         0.72        10.19         6.05         4.73 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       13.97        10.98        11.01        12.99        13.97         7.10 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 
       30.05        13.05        10.06        41.36        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 
        2.40        20.55        17.69        16.31        16.41        14.86 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.39         0.66         0.76        18.28        26.43 

$`DEL PEAK 46(22Q13.32) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       17.79        37.05        37.25        16.04        32.45        32.91 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       14.93        36.03        53.00        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       26.01        24.00        20.98        34.03        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
        0.99        34.98        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       35.01        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
        5.19         6.87        75.25        50.37        58.39        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01        11.74         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       13.02        22.03        22.98        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       12.95        13.05        11.08        12.03        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       11.51        20.42        17.75        18.25         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       16.14        15.58        12.39        10.13        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB 
       24.43        38.20        92.75        49.91         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       55.04        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV 
       13.78        35.80        26.17        47.15        52.80         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         1.32         5.19         5.49        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       14.76        67.00        24.13        17.95        17.23        43.04 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        37.74        10.39         8.45        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       11.84        36.03         8.02         1.02        46.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 
        0.99        32.98         0.99         0.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 
       13.02        35.01        14.01        48.03        32.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
       17.03         0.99        20.98        13.94         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-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       64.01        51.98        49.97        61.97        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.69         4.60         1.81         6.05         6.97         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       60.03         7.99        15.02        12.00        15.02        36.00 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.95         5.29       126.44        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        0.49        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       11.97         8.45         9.96        37.51        31.30         1.02 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.46        55.76        47.08 

  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                          15.52                           19.02 
[1] "0.2 - 140.4 (15.5)" "0.1 - 139.2 (19.0)"
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   153  66
  DEL PEAK 46(22Q13.32) WILD-TYPE 285  96
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    153   66
  DEL PEAK 46(22Q13.32) WILD-TYPE  285   96
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON                            153                             285
  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        28        0        9        58         1
  DEL PEAK 46(22Q13.32) WILD-TYPE      74        1       27       113         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(22Q13.32) MUTATED           1        10         12         30
  DEL PEAK 46(22Q13.32) WILD-TYPE         2        16          9         48
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(22Q13.32) MUTATED           23       33        11         0
  DEL PEAK 46(22Q13.32) WILD-TYPE         30       28        16         2
D73V4, multiclass
            clus
vv           DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  STAGE I                               28                              74
  STAGE IA                               0                               1
  STAGE II                               9                              27
  STAGE IIA                             58                             113
  STAGE IIB                              1                               9
  STAGE IIC                              1                               2
  STAGE III                             10                              16
  STAGE IIIA                            12                               9
  STAGE IIIB                            30                              48
  STAGE IIIC                            23                              30
  STAGE IV                              33                              28
  STAGE IVA                             11                              16
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 46(22Q13.32) MUTATED     4  36 156  26
  DEL PEAK 46(22Q13.32) WILD-TYPE  16  69 256  39
D73V5, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  T1                             4                              16
  T2                            36                              69
  T3                           156                             256
  T4                            26                              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 46(22Q13.32) MUTATED   102  70  49
  DEL PEAK 46(22Q13.32) WILD-TYPE 239  78  63
D73V6, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  N0                           102                             239
  N1                            70                              78
  N2                            49                              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 46(22Q13.32) MUTATED   152  39   4   0  23
  DEL PEAK 46(22Q13.32) WILD-TYPE 294  35   6   2  40
D73V7, multiclass
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  M0                            152                             294
  M1                             39                              35
  M1A                             4                               6
  M1B                             0                               2
  MX                             23                              40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED    99 123
  DEL PEAK 46(22Q13.32) WILD-TYPE 184 198
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED     99  123
  DEL PEAK 46(22Q13.32) WILD-TYPE  184  198
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  FEMALE                            99                             184
  MALE                             123                             198
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                    143
  DEL PEAK 46(22Q13.32) WILD-TYPE                  235
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                              10
  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
D73V9, multiclass
                                clus
vv                               DEL PEAK 46(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                     143
  COLON MUCINOUS ADENOCARCINOMA                             10
  RECTAL ADENOCARCINOMA                                     62
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       235
  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"
D73V10, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED     4 218
  DEL PEAK 46(22Q13.32) WILD-TYPE   5 377
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED      4  218
  DEL PEAK 46(22Q13.32) WILD-TYPE    5  377
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  NO                              4                               5
  YES                           218                             377
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(22Q13.32) MUTATED   151   2  17  12
  DEL PEAK 46(22Q13.32) WILD-TYPE 285   3  19  17
D73V11, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  R0                           151                             285
  R1                             2                               3
  R2                            17                              19
  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                          21   101
  DEL PEAK 46(22Q13.32) WILD-TYPE                        35   191
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 46(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 46(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     35
  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"
