[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/15076882/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/15089877/transformed.cor.cli.txt"

nPatients in clinical file=624, in cluster file=615, common to both=608
[1]  73 608
[1] "AMP PEAK  1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          144                           464 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          144                           464 
[1] "AMP PEAK  2(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          138                           470 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          138                           470 
[1] "AMP PEAK  3(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         492 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         492 
[1] "AMP PEAK  4(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           64                           544 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           64                           544 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          154                           454 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          154                           454 
[1] "AMP PEAK  6(7P21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          359                           249 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          359                           249 
[1] "AMP PEAK  7(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           209                            399 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           209                            399 
[1] "AMP PEAK  8(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           253                            355 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           253                            355 
[1] "AMP PEAK  9(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          326                           282 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          326                           282 
[1] "AMP PEAK 10(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           363                            245 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           363                            245 
[1] "AMP PEAK 11(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            39                            569 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            39                            569 
[1] "AMP PEAK 12(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           136                            472 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           136                            472 
[1] "AMP PEAK 13(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            150                             458 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            150                             458 
[1] "AMP PEAK 14(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            396                             212 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            396                             212 
[1] "AMP PEAK 15(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           391                            217 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           391                            217 
[1] "AMP PEAK 16(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           394                            214 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           394                            214 
[1] "AMP PEAK 17(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            566 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            42                            566 
[1] "AMP PEAK 18(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           170                            438 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           170                            438 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         158                          450 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         158                          450 
[1] "AMP PEAK 20(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           142                            466 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           142                            466 
[1] "AMP PEAK 21(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           111                            497 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           111                            497 
[1] "AMP PEAK 22(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         138                          470 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         138                          470 
[1] "AMP PEAK 23(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           277                            331 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           277                            331 
[1] "AMP PEAK 24(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            359                             249 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            359                             249 
[1] "AMP PEAK 25(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            463                             145 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            463                             145 
[1] "AMP PEAK 26(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         465                          143 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         465                          143 
[1] "AMP PEAK 27(20Q13.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            468                             140 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            468                             140 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           240                            368 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           240                            368 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        173                         435 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        173                         435 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          172                           436 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          172                           436 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         587 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         587 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           573 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           573 
[1] "DEL PEAK  6(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           90                           518 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           90                           518 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          116                           492 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          116                           492 
[1] "DEL PEAK  8(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            62                            546 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            62                            546 
[1] "DEL PEAK  9(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          196                           412 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          196                           412 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          218                           390 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          218                           390 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          227                           381 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          227                           381 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          156                           452 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          156                           452 
[1] "DEL PEAK 13(5Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          184                           424 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          184                           424 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          186                           422 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          186                           422 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           530 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           530 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         517 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         91                         517 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           592 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           592 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          286                           322 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          286                           322 
[1] "DEL PEAK 19(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        299                         309 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        299                         309 
[1] "DEL PEAK 20(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           561 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           47                           561 
[1] "DEL PEAK 21(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           82                           526 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           82                           526 
[1] "DEL PEAK 22(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            496 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           112                            496 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           135                            473 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           135                            473 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            158                             450 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            158                             450 
[1] "DEL PEAK 25(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           154                            454 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           154                            454 
[1] "DEL PEAK 26(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           110                            498 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           110                            498 
[1] "DEL PEAK 27(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            91                            517 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            91                            517 
[1] "DEL PEAK 28(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             88                             520 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             88                             520 
[1] "DEL PEAK 29(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           207                            401 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           207                            401 
[1] "DEL PEAK 30(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           213                            395 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           213                            395 
[1] "DEL PEAK 31(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           249                            359 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           249                            359 
[1] "DEL PEAK 32(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           247                            361 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           247                            361 
[1] "DEL PEAK 33(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           244                            364 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           244                            364 
[1] "DEL PEAK 34(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            234                             374 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            234                             374 
[1] "DEL PEAK 35(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            67                            541 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            67                            541 
[1] "DEL PEAK 36(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            81                            527 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            81                            527 
[1] "DEL PEAK 37(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         364                          244 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         364                          244 
[1] "DEL PEAK 38(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            95                            513 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            95                            513 
[1] "DEL PEAK 39(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            365                             243 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            365                             243 
[1] "DEL PEAK 40(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           410                            198 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           410                            198 
[1] "DEL PEAK 41(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           427                            181 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           427                            181 
[1] "DEL PEAK 42(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           422                            186 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           422                            186 
[1] "DEL PEAK 43(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            96                            512 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            96                            512 
[1] "DEL PEAK 44(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           132                            476 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           132                            476 
[1] "DEL PEAK 45(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           210                            398 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           210                            398 
[1] "DEL PEAK 46(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            225                             383 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            225                             383 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "COMPLETENESS_OF_RESECTION"             
[18] "NUMBER_OF_LYMPH_NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 608 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=99,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=345,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
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:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "347"                 
freq.contrast "347"              "2"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=38,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 608 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [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"                                  
YEARS_TO_BIRTH, 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 
 20 107 413  66 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 107 413  66 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 107 413  66 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 107 413  66 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
342 149 114 
[1] "table(vv)"
vv
 N0  N1  N2 
342 149 114 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
342 149 114 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
342 149 114 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
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   106  32
  AMP PEAK  1(1Q31.1) WILD-TYPE 362  83
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          138                           445 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                           32                            83 
$`AMP PEAK  1(1Q31.1) MUTATED`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       11.47        43.76        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 
       16.57        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        56.25         5.03        38.99        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-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        10.06        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 
       10.98        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        22.42        14.50         0.20        17.85         5.65 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       22.36        65.00        12.10        11.74         2.24         3.06 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5349 
        0.26        49.08        37.02        25.02        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-5539 
       15.02         5.03        15.02        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        65.85        39.42        18.18         9.93 
TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-4110 
       42.77         9.70        30.28        24.13        13.55        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 
       15.39        10.39        32.02        46.03        34.03         6.05 
TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       19.99        19.99        28.04        23.01        37.02        36.03 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       31.00        70.03        51.98         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 
        0.49         0.69         0.72        10.19         9.37         4.73 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
       11.01        13.97        15.02       129.27        24.13        32.61 
TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       20.55         8.61        10.78        13.64        11.97         9.96 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.39         0.69         0.76        18.28        47.08        26.43 

$`AMP PEAK  1(1Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       11.47         4.80        46.65        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        13.94        37.05        37.25        37.02        34.65 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 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-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        19.99        61.02         6.05         6.97 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       14.01         0.92        50.04        11.01         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       24.03        29.98        18.05        31.00         2.01        24.00 
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-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02         1.02        33.04        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-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        41.00        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         5.79        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.20        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        15.75        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84        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        45.40        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        43.27 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 
        4.80        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        13.25 
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 
       67.30        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        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       13.05        12.00        29.46        32.98         8.42        31.30 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       70.03        39.48        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       20.05        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-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-3878 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99         0.99         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-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        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-A014 
        0.99        20.98        13.94         6.02        25.97        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        9.07         1.02        12.00        64.01        10.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       61.97        41.00         1.45        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.97        13.97        78.12         7.17        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        36.00        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       57.24        51.48         0.49         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       16.41        11.51        17.46         8.45        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       28.57        32.19         0.66         0.53         1.12         0.46 
TCGA-G5-6235 
       55.76 

  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                        19.99                         19.04 
[1] "0.2 - 129.3 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    95  47
  AMP PEAK  1(1Q31.1) WILD-TYPE 347 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     95   47
  AMP PEAK  1(1Q31.1) WILD-TYPE  347  115
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON                           95                           347
  RECTUM                          47                           115
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(1Q31.1) MUTATED        18        0        7        35         2
  AMP PEAK  1(1Q31.1) WILD-TYPE      86        1       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         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(1Q31.1) MUTATED           17       21         8         0
  AMP PEAK  1(1Q31.1) WILD-TYPE         37       40        19         2
D1V4, multiclass
            clus
vv           AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  STAGE I                             18                            86
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           35                           136
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           7                            14
  STAGE IIIB                          18                            61
  STAGE IIIC                          17                            37
  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  22  96  21
  AMP PEAK  1(1Q31.1) WILD-TYPE  16  85 317  45
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  T1                           4                            16
  T2                          22                            85
  T3                          96                           317
  T4                          21                            45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(1Q31.1) MUTATED    69  38  34
  AMP PEAK  1(1Q31.1) WILD-TYPE 273 111  80
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  N0                          69                           273
  N1                          38                           111
  N2                          34                            80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    96  28
  AMP PEAK  1(1Q31.1) WILD-TYPE 352  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     96   28
  AMP PEAK  1(1Q31.1) WILD-TYPE  352   58
   clus
vv  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  0                          96                           352
  1                          28                            58
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    61  83
  AMP PEAK  1(1Q31.1) WILD-TYPE 225 239
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     61   83
  AMP PEAK  1(1Q31.1) WILD-TYPE  225  239
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  FEMALE                          61                           225
  MALE                            83                           239
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                     86
  AMP PEAK  1(1Q31.1) WILD-TYPE                  295
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                               9
  AMP PEAK  1(1Q31.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                      43
  AMP PEAK  1(1Q31.1) WILD-TYPE                   103
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                                3
  AMP PEAK  1(1Q31.1) WILD-TYPE                             10
D1V9, multiclass
                                clus
vv                               AMP PEAK  1(1Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    86
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   43
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     295
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                    103
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED     5 139
  AMP PEAK  1(1Q31.1) WILD-TYPE   4 460
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED      5  139
  AMP PEAK  1(1Q31.1) WILD-TYPE    4  460
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  NO                            5                             4
  YES                         139                           460
[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 340   4  25  23
D1V11, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  R0                          99                           340
  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                          14    78
  AMP PEAK  1(1Q31.1) WILD-TYPE                        46   214
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     78
                                  clus
vv                                 AMP PEAK  1(1Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   46
  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  30
  AMP PEAK  2(2Q33.1) WILD-TYPE 367  85
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          131                           452 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                           30                            85 
$`AMP PEAK  2(2Q33.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       11.47        43.76        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        10.06        35.05 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3979 TCGA-AA-A00W 
       33.07         0.00        24.03        16.08        24.00        14.99 
TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6548 TCGA-AD-6888 
       31.00         1.02        26.01         2.96        21.37         4.21 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 
        5.79        22.42        27.42         0.20        16.44        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 
        0.20        18.84         5.13         3.19         0.07         0.26 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 
       40.34        21.99         8.02        29.06         5.03        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 
       15.02        14.04        29.03        21.99        14.99        45.40 
TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA 
       11.51         4.80        17.13         7.53        24.43         7.50 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 
        7.76        14.04        26.47        35.97         8.61         1.55 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 
        8.35        74.56        45.11        39.42        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL 
       18.18        12.79        13.05        29.46        32.98        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       24.13        39.48        17.23        10.39        16.83        15.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 
       86.63        65.98        36.03        46.03         6.05        19.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       19.99         1.02        17.03         1.02        48.03        28.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 
        1.02         0.99        12.00        31.00        70.03        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-4957 TCGA-CL-5917 
        0.49         0.69        26.43        10.19        13.97        78.12 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 
        7.17        12.99        12.00        15.02        36.00        13.05 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 
      129.27         2.40        20.91        16.31        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
       37.51         0.76         0.46        18.28        47.08 

$`AMP PEAK  2(2Q33.1) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 
       16.57        37.05        37.25        37.02        32.45        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 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-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       21.76        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1.02        37.05        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03        10.06         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        17.03        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        10.98        32.02        12.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04        35.01 
TCGA-AA-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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 
        0.07        56.55         0.79         0.72        10.88         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-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         3.29         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        70.16        15.62        49.08 
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-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       15.02        12.00        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       15.12        17.85        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        51.75 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       13.78        35.80        26.17        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        12.00        42.77 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
        8.42        31.30         9.70        70.03        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        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        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        10.98        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        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       18.180                        19.215 
[1] "0.0 - 129.3 (18.2)" "0.0 - 140.4 (19.2)"
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    89  49
  AMP PEAK  2(2Q33.1) WILD-TYPE 353 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     89   49
  AMP PEAK  2(2Q33.1) WILD-TYPE  353  113
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON                           89                           353
  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      83        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         58
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(2Q33.1) MUTATED           22       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                            83
  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                            58
  STAGE IIIC                          22                            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  97  14
  AMP PEAK  2(2Q33.1) WILD-TYPE  17  84 316  52
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  T1                           3                            17
  T2                          23                            84
  T3                          97                           316
  T4                          14                            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  2(2Q33.1) MUTATED    61  34  41
  AMP PEAK  2(2Q33.1) WILD-TYPE 281 115  73
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  N0                          61                           281
  N1                          34                           115
  N2                          41                            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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    92  22
  AMP PEAK  2(2Q33.1) WILD-TYPE 356  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     92   22
  AMP PEAK  2(2Q33.1) WILD-TYPE  356   64
   clus
vv  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  0                          92                           356
  1                          22                            64
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    66  72
  AMP PEAK  2(2Q33.1) WILD-TYPE 220 250
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     66   72
  AMP PEAK  2(2Q33.1) WILD-TYPE  220  250
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  FEMALE                          66                           220
  MALE                            72                           250
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                     79
  AMP PEAK  2(2Q33.1) WILD-TYPE                  302
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                              10
  AMP PEAK  2(2Q33.1) WILD-TYPE                            50
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                      49
  AMP PEAK  2(2Q33.1) WILD-TYPE                    97
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                                0
  AMP PEAK  2(2Q33.1) WILD-TYPE                             13
D2V9, multiclass
                                clus
vv                               AMP PEAK  2(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                    79
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     302
  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     4 134
  AMP PEAK  2(2Q33.1) WILD-TYPE   5 465
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED      4  134
  AMP PEAK  2(2Q33.1) WILD-TYPE    5  465
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  NO                            4                             5
  YES                         134                           465
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2Q33.1) MUTATED    94   2   8   9
  AMP PEAK  2(2Q33.1) WILD-TYPE 345   3  28  20
D2V11, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  R0                          94                           345
  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                          19    73
  AMP PEAK  2(2Q33.1) WILD-TYPE                        41   219
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     73
                                  clus
vv                                 AMP PEAK  2(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   41
  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 382  89
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        112                         471 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                         26                          89 
$`AMP PEAK  3(5P12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 
       11.47        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        19.04        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        10.98        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         5.79        16.44         0.92         0.20        18.84 
TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 
        5.65        62.79        49.41        29.56         1.94         2.24 
TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       49.08        25.02        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        12.79 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
        8.42        30.28        24.13        37.74        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3731 
       86.63        65.98        36.03        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        10.98 
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 
       28.57        32.19         0.53         0.76 

$`AMP PEAK  3(5P12) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        4.80        11.47        43.76        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 
       42.28        35.11        13.94        16.57        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 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        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       29.00         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 
        0.92        50.04        47.05        15.02        11.01        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        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
        0.00        32.05        31.07        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
        2.01        16.08        13.05        34.06        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02        39.06        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.20         0.46        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       15.75        21.44        17.82        17.26        17.85        19.33 
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        45.40 
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        43.27        15.12        17.85         4.80        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         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        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       13.05        12.00        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        9.70        70.03        39.48        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        16.83        15.39 
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 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02        19.99        14.04         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
       13.94         6.02        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.97         0.49         1.45        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         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-6154 
       78.12         7.17        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       13.97        36.00        30.05        12.95        13.05         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.34        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.39         0.66         0.69         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        0.2                         0.0 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      95.18                      140.38 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      18.92                       19.10 
[1] "0.2 - 95.2 (18.9)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    76  40
  AMP PEAK  3(5P12) WILD-TYPE 366 122
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     76   40
  AMP PEAK  3(5P12) WILD-TYPE  366  122
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  COLON                         76                         366
  RECTUM                        40                         122
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5P12) MUTATED        18        0        6        27         1
  AMP PEAK  3(5P12) WILD-TYPE      86        1       30       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         67
                             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         38       44        21         1
D3V4, multiclass
            clus
vv           AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  STAGE I                           18                          86
  STAGE IA                           0                           1
  STAGE II                           6                          30
  STAGE IIA                         27                         144
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          3                          23
  STAGE IIIA                         5                          16
  STAGE IIIB                        12                          67
  STAGE IIIC                        16                          38
  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  82 337  53
D3V5, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  T1                         2                          18
  T2                        25                          82
  T3                        76                         337
  T4                        13                          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  3(5P12) MUTATED    54  32  29
  AMP PEAK  3(5P12) WILD-TYPE 288 117  85
D3V6, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  N0                        54                         288
  N1                        32                         117
  N2                        29                          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"
D3V7, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    78  23
  AMP PEAK  3(5P12) WILD-TYPE 370  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     78   23
  AMP PEAK  3(5P12) WILD-TYPE  370   63
   clus
vv  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  0                        78                         370
  1                        23                          63
[1] 2 2
[1] FALSE
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    52  64
  AMP PEAK  3(5P12) WILD-TYPE 234 258
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     52   64
  AMP PEAK  3(5P12) WILD-TYPE  234  258
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  FEMALE                        52                         234
  MALE                          64                         258
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                     67
  AMP PEAK  3(5P12) WILD-TYPE                  314
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                               9
  AMP PEAK  3(5P12) WILD-TYPE                            51
                             vv
clus                          RECTAL ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                      40
  AMP PEAK  3(5P12) WILD-TYPE                   106
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                                0
  AMP PEAK  3(5P12) WILD-TYPE                             13
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                                   314
  COLON MUCINOUS ADENOCARCINOMA                           51
  RECTAL ADENOCARCINOMA                                  106
  RECTAL MUCINOUS ADENOCARCINOMA                          13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED     3 113
  AMP PEAK  3(5P12) WILD-TYPE   6 486
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED      3  113
  AMP PEAK  3(5P12) WILD-TYPE    6  486
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  NO                          3                           6
  YES                       113                         486
[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 355   4  23  26
D3V11, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  R0                        84                         355
  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                        47   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                                 47
  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    55   7
  AMP PEAK  4(5Q22.3) WILD-TYPE 413 108
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           62                           521 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                            7                           108 
$`AMP PEAK  4(5Q22.3) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       11.47        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        19.04 
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         5.79        16.44        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        15.65 
TCGA-QL-A97D TCGA-AF-6655 TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A00H 
        9.70        20.02        19.99         1.02         1.02        25.97 
TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       15.95        12.00        31.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
        0.72        10.06        20.55        16.31        11.51        11.97 
TCGA-F5-6465 TCGA-F5-6811 
       37.51        32.19 

$`AMP PEAK  4(5Q22.3) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.02        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        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-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-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-3680 TCGA-AA-3685 
        0.92        50.04        47.05        47.01        11.01        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-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       21.99        16.08        50.99        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84        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        49.08        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        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-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 
       45.40        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        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       65.85        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 
       18.18        10.98        19.33        19.33         9.93        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        30.28        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       14.50        16.83        15.39        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-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-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        23.01        37.02        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 
        1.94        38.96        61.97        41.00         1.45        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         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        78.12         7.17        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-DT-5265 TCGA-DY-A0XA 
       10.98        30.05        12.95        13.05         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-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.34        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         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  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                         0.49                          0.00 
  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 
                        15.98                         19.33 
[1] "0.5 - 130.7 (16.0)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.6"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    44  20
  AMP PEAK  4(5Q22.3) WILD-TYPE 398 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     44   20
  AMP PEAK  4(5Q22.3) WILD-TYPE  398  142
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON                           44                           398
  RECTUM                          20                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(5Q22.3) MUTATED         9        0        2        16         1
  AMP PEAK  4(5Q22.3) WILD-TYPE      95        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         71
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(5Q22.3) MUTATED            7        9         5         0
  AMP PEAK  4(5Q22.3) WILD-TYPE         47       52        22         2
D4V4, multiclass
            clus
vv           AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  STAGE I                              9                            95
  STAGE IA                             0                             1
  STAGE II                             2                            34
  STAGE IIA                           16                           155
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            1                            25
  STAGE IIIA                           2                            19
  STAGE IIIB                           8                            71
  STAGE IIIC                           7                            47
  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  12  44   7
  AMP PEAK  4(5Q22.3) WILD-TYPE  19  95 369  59
D4V5, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  T1                           1                            19
  T2                          12                            95
  T3                          44                           369
  T4                           7                            59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  4(5Q22.3) MUTATED    31  17  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 311 132  99
D4V6, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  N0                          31                           311
  N1                          17                           132
  N2                          15                            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    41  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 407  71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     41   15
  AMP PEAK  4(5Q22.3) WILD-TYPE  407   71
   clus
vv  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  0                          41                           407
  1                          15                            71
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    31  33
  AMP PEAK  4(5Q22.3) WILD-TYPE 255 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     31   33
  AMP PEAK  4(5Q22.3) WILD-TYPE  255  289
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  FEMALE                          31                           255
  MALE                            33                           289
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                     41
  AMP PEAK  4(5Q22.3) WILD-TYPE                  340
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                               3
  AMP PEAK  4(5Q22.3) WILD-TYPE                            57
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                      20
  AMP PEAK  4(5Q22.3) WILD-TYPE                   126
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                                0
  AMP PEAK  4(5Q22.3) WILD-TYPE                             13
D4V9, multiclass
                                clus
vv                               AMP PEAK  4(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                    41
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   20
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     340
  COLON MUCINOUS ADENOCARCINOMA                             57
  RECTAL ADENOCARCINOMA                                    126
  RECTAL MUCINOUS ADENOCARCINOMA                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED     1  63
  AMP PEAK  4(5Q22.3) WILD-TYPE   8 536
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED      1   63
  AMP PEAK  4(5Q22.3) WILD-TYPE    8  536
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  NO                            1                             8
  YES                          63                           536
[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 395   5  29  29
D4V11, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  R0                          44                           395
  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                           8    34
  AMP PEAK  4(5Q22.3) WILD-TYPE                        52   258
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  4(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   52
  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   114  28
  AMP PEAK  5(6P21.1) WILD-TYPE 354  87
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          142                           441 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           28                            87 
$`AMP PEAK  5(6P21.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       43.43        44.91        36.53        32.45        30.44        29.19 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A56B 
       22.52        25.08        25.18        20.61        23.87        56.25 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3561 
       29.00        29.00        12.99        13.02        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       19.99         2.01        15.02        37.05        85.05        10.06 
TCGA-AA-3812 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 
       35.05        17.03        10.06        24.03        27.02         2.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F 
       20.98        21.99        27.02         7.96        13.94        34.03 
TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 
       27.02        31.00         2.96        40.96        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 
       14.50         0.95         0.20        17.26         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-QG-A5YW TCGA-QL-A97D 
       91.79        46.75        10.98        12.79        29.46         9.70 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       30.28        24.13        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       14.50        15.39        65.98        36.03        24.00        46.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 
        6.05        19.99        19.99        29.98         1.02         1.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       14.04         1.02         0.99        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 
       31.00         0.72        10.19         6.05         9.37        10.98 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       12.99        12.00        15.02        36.00        13.05       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 
       24.13        51.48        20.55        15.85        17.69        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 TCGA-G5-6641 
       28.57         0.39        18.28        26.43 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        24.33        42.28        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       16.57        37.05        37.25        37.02        34.65        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-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       32.71        29.16        27.09        24.13         8.38        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-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
        0.00        19.07        34.03        26.01         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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 
       38.99        36.95        37.02        14.93         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        25.02        24.00        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31        15.75        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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        49.08        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 
       25.02        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 
       45.40        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 
       43.27        17.85         4.80        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        13.25        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        67.30        65.85 
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        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        13.05        12.00        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
        8.42        31.30        70.03        39.48        17.23        13.55 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       12.72        16.83        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        20.05 
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        26.43         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        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        13.97        10.98        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 
       32.19         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 
                          0.2                           0.0 
  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 
                       17.195                        19.330 
[1] "0.2 - 129.3 (17.2)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   100  51
  AMP PEAK  5(6P21.1) WILD-TYPE 342 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    100   51
  AMP PEAK  5(6P21.1) WILD-TYPE  342  111
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  COLON                          100                           342
  RECTUM                          51                           111
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(6P21.1) MUTATED        21        0        4        33         1
  AMP PEAK  5(6P21.1) WILD-TYPE      83        1       32       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         54
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(6P21.1) MUTATED           20       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                             21                            83
  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                            54
  STAGE IIIC                          20                            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  20 113  15
  AMP PEAK  5(6P21.1) WILD-TYPE  14  87 300  51
D5V5, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  T1                           6                            14
  T2                          20                            87
  T3                         113                           300
  T4                          15                            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  5(6P21.1) MUTATED    67  41  45
  AMP PEAK  5(6P21.1) WILD-TYPE 275 108  69
D5V6, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  N0                          67                           275
  N1                          41                           108
  N2                          45                            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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   102  31
  AMP PEAK  5(6P21.1) WILD-TYPE 346  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    102   31
  AMP PEAK  5(6P21.1) WILD-TYPE  346   55
   clus
vv  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  0                         102                           346
  1                          31                            55
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    65  89
  AMP PEAK  5(6P21.1) WILD-TYPE 221 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     65   89
  AMP PEAK  5(6P21.1) WILD-TYPE  221  233
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                          65                           221
  MALE                            89                           233
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                     91
  AMP PEAK  5(6P21.1) WILD-TYPE                  290
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                               9
  AMP PEAK  5(6P21.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                      50
  AMP PEAK  5(6P21.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                1
  AMP PEAK  5(6P21.1) WILD-TYPE                             12
D5V9, multiclass
                                clus
vv                               AMP PEAK  5(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                    91
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  5(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     290
  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     7 147
  AMP PEAK  5(6P21.1) WILD-TYPE   2 452
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      7  147
  AMP PEAK  5(6P21.1) WILD-TYPE    2  452
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  NO                            7                             2
  YES                         147                           452
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(6P21.1) MUTATED   107   0  14   5
  AMP PEAK  5(6P21.1) WILD-TYPE 332   5  22  24
D5V11, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  R0                         107                           332
  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                          15    82
  AMP PEAK  5(6P21.1) WILD-TYPE                        45   210
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     82
                                  clus
vv                                 AMP PEAK  5(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   45
  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  70
  AMP PEAK  6(7P21.3) WILD-TYPE 195  45
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                          343                           240 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                           70                            45 
$`AMP PEAK  6(7P21.3) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        45.60        13.94        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.19        29.16        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 
       24.16        20.61        24.69        23.87        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       24.92        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 
       37.05         1.02        35.01        58.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07        36.03         0.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       14.01        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
        5.03        85.05        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        10.06         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       31.00        24.00        24.00        20.98        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        26.01        27.02        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01F 
       34.03        38.04        42.02        17.03        15.02        32.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       33.04        26.01        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
        5.03         0.92        39.98        40.96        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         5.79        22.42        27.42         0.20        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 
       17.82        17.26        18.84        75.25        50.37        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-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         3.29         1.35        17.56       102.44        40.34 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       21.99        20.02        25.02         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        15.02        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       11.01        10.06        19.59        11.51        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 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-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       10.26        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 
      140.38         7.50        44.32       131.51         7.76         6.12 
TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       14.04        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       13.45         1.55        33.67         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       28.21        82.39        23.51        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        13.78        91.79        46.75        47.15        18.18 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-QL-A97D 
        9.93        15.65        12.79        13.05         8.42         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 
       30.28        70.03        24.13        39.48        17.23        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        16.83        15.39        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       86.63        65.98         7.07        36.03        24.00        46.03 
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-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 
       29.98         0.99         0.99        19.99        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        1.02        48.03        19.99        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99         6.02        25.97        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A026 
        1.02        12.00        31.00        70.03        10.98         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.96        38.04         0.49         0.69         0.72        26.43 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       10.19         6.05         6.05         9.37         4.73        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        10.98        11.01        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        36.00        10.98        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
      126.44        41.36        57.24       129.27        24.13         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.31        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       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        42.90        24.33        42.28        16.57        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        19.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       17.98        15.95        38.99         0.00        17.03         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3939 
       33.07        36.03        31.07        53.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 
       33.01        26.01         2.01        34.03         2.01        50.99 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A 
       13.05        25.02        24.00        19.07         7.96        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        21.99        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
       35.01        39.06        39.98        22.03        41.00        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
        0.07        56.55         0.72        10.88         0.92        27.09 
TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       21.44        17.85        19.33        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5254 
       32.94         5.13         6.77       100.01        11.74         2.24 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
        0.07         0.26         0.33         0.10        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       49.08        51.32        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       23.05        37.02        26.04        30.08        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       21.99        13.02        14.04        12.95        13.05        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       45.40        12.26        13.51        20.19        20.42        18.25 
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-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1HB 
       12.00        11.38       119.70       130.65        13.32       135.65 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
      139.17        26.47        81.37       119.93        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 
       16.24        13.25        19.43         8.35        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       51.75        22.09        26.04        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98        19.33        19.33        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-6672 
       32.98        31.30        43.04        13.55        19.10        10.39 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         8.02        20.05 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 
        1.02        34.03         2.01        50.04         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02        32.98         1.02        36.95        13.02        14.01 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y 
       32.02        28.04        14.04        20.98        13.94        23.01 
TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       37.02        64.01        51.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 
        1.45         1.81         6.97        13.97        15.02        30.05 
TCGA-DC-6681 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       12.95        51.48        32.61        20.55        19.96        17.00 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       16.41         8.61        17.46        37.51         0.53         1.12 

  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                            0                             0 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE 
                        17.85                         19.81 
[1] "0.0 - 140.4 (17.9)" "0.0 - 139.2 (19.8)"
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   249 108
  AMP PEAK  6(7P21.3) WILD-TYPE 193  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    249  108
  AMP PEAK  6(7P21.3) WILD-TYPE  193   54
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  COLON                          249                           193
  RECTUM                         108                            54
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(7P21.3) MUTATED        57        1       19        77         3
  AMP PEAK  6(7P21.3) WILD-TYPE      47        0       17        94         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(7P21.3) MUTATED           2        15         15         59
  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         16       19         6         1
D6V4, multiclass
            clus
vv           AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  STAGE I                             57                            47
  STAGE IA                             1                             0
  STAGE II                            19                            17
  STAGE IIA                           77                            94
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           15                            11
  STAGE IIIA                          15                             6
  STAGE IIIB                          59                            20
  STAGE IIIC                          38                            16
  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  61 244  39
  AMP PEAK  6(7P21.3) WILD-TYPE   7  46 169  27
D6V5, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  T1                          13                             7
  T2                          61                            46
  T3                         244                           169
  T4                          39                            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   171 108  77
  AMP PEAK  6(7P21.3) WILD-TYPE 171  41  37
D6V6, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  N0                         171                           171
  N1                         108                            41
  N2                          77                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   250  61
  AMP PEAK  6(7P21.3) WILD-TYPE 198  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    250   61
  AMP PEAK  6(7P21.3) WILD-TYPE  198   25
   clus
vv  AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  0                         250                           198
  1                          61                            25
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P21.3) MUTATED   168 191
  AMP PEAK  6(7P21.3) WILD-TYPE 118 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED    168  191
  AMP PEAK  6(7P21.3) WILD-TYPE  118  131
        clus
vv       AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  FEMALE                         168                           118
  MALE                           191                           131
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                    224
  AMP PEAK  6(7P21.3) WILD-TYPE                  157
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(7P21.3) MUTATED                              25
  AMP PEAK  6(7P21.3) WILD-TYPE                            35
                               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                                   224
  COLON MUCINOUS ADENOCARCINOMA                           25
  RECTAL ADENOCARCINOMA                                  102
  RECTAL MUCINOUS ADENOCARCINOMA                           5
                                clus
vv                               AMP PEAK  6(7P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     157
  COLON MUCINOUS ADENOCARCINOMA                             35
  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     8 351
  AMP PEAK  6(7P21.3) WILD-TYPE   1 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P21.3) MUTATED      8  351
  AMP PEAK  6(7P21.3) WILD-TYPE    1  248
     clus
vv    AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  NO                            8                             1
  YES                         351                           248
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(7P21.3) MUTATED   257   4  25  14
  AMP PEAK  6(7P21.3) WILD-TYPE 182   1  11  15
D6V11, multiclass
    clus
vv   AMP PEAK  6(7P21.3) MUTATED AMP PEAK  6(7P21.3) WILD-TYPE
  R0                         257                           182
  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                          40   183
  AMP PEAK  6(7P21.3) WILD-TYPE                        20   109
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(7P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    183
                                  clus
vv                                 AMP PEAK  6(7P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   20
  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   156  42
  AMP PEAK  7(8P11.23) WILD-TYPE 312  73
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                           198                            385 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                            42                             73 
$`AMP PEAK  7(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 
       11.47        11.47        43.43        24.33        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-3529 
       35.01         6.97         1.02        36.03        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3562 
       29.00        26.01        12.99        33.99        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-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3713 
       47.01         5.98        37.05        19.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 
       19.04        10.06        36.95        17.03         0.00        31.07 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 
       31.07        24.03        18.05        12.99        24.00        34.06 
TCGA-AA-3979 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S 
       24.00        18.05         0.99        21.99        10.98         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 
       37.02        51.98         0.92         0.07         5.79        27.42 
TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 
       16.44        27.09        16.31        21.44        17.26         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-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       49.41         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        3.29         0.07       102.44        15.62        49.08        51.32 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 
        2.01        20.02        37.02        25.02         8.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       16.01        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       29.03        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.08        10.06        11.51        20.19         1.32 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
        4.80        17.13        16.14         7.53        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA 
        9.04        11.38        10.26       119.70        38.20         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 
       44.32         6.12       117.07        98.24        13.45         6.18 
TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6311 
       16.24        67.30        65.85        53.62        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YW 
       26.43        46.75        47.15        18.18        15.65        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-3911 TCGA-AF-6655 
       32.98         8.42        30.28        70.03        37.74        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3594 
       10.39        65.98        36.03        36.03        24.00         2.01 
TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
        0.99        36.95        35.01         1.02        48.03        32.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       36.03         1.02         0.99        15.95        31.00        51.98 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 
       38.04         0.49         0.69         0.72         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        4.73        78.12         7.17        15.02        36.00        10.98 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       13.05        41.36        57.24        24.13        51.48         0.49 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6465 
       17.00        15.85        16.31        11.51        10.78        37.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
       28.57        32.19         0.69         0.46        18.28        47.08 

$`AMP PEAK  7(8P11.23) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        4.80        43.76        46.65        43.76        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3510 
        5.03         7.04         3.02         1.02        58.03        63.98 
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-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 
        8.05        19.07        34.03        29.00         0.99        14.01 
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-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 
       19.99        13.94        61.02         2.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01        36.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05         0.99        53.00        17.03        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-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        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-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-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-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        10.88         0.20         0.46         0.92        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
        0.95        15.75         0.20        17.82        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4684 
       18.84        75.25        50.37        58.39         1.41        65.00 
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-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       40.34        70.16        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       23.05        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 
       30.08        17.03        12.00        14.04        16.04        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.26        19.59        13.51        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 
       43.27        15.12        17.85        12.49        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       10.13         9.44        11.64        13.41         1.51        12.00 
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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M 
       26.47        81.37       119.93        35.97        60.79        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.38        11.11        13.64        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        33.67        13.25         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-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       74.56        44.68        55.04        51.75        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       91.79        52.80        10.98        19.33        19.33         9.93 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.79        13.05        12.00        42.77        31.30         9.70 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       12.72        10.39        14.50        16.83        15.39        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       11.84        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        13.02        14.01        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       37.02        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       41.00         1.45        26.43         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        6.97        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       12.00        13.97        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      126.44       129.27        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       20.91        18.28        17.69        16.34        16.41         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
        0.39         0.66         0.53         1.12         0.76        55.76 
TCGA-G5-6641 
       26.43 

  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                             0                              0 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                        119.70                         140.38 
  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE 
                         18.64                          19.33 
[1] "0.0 - 119.7 (18.6)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   156  53
  AMP PEAK  7(8P11.23) WILD-TYPE 286 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    156   53
  AMP PEAK  7(8P11.23) WILD-TYPE  286  109
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  COLON                           156                            286
  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      67        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         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.23) MUTATED           24       22         9         0
  AMP PEAK  7(8P11.23) WILD-TYPE         30       39        18         2
D7V4, multiclass
            clus
vv           AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  STAGE I                              37                             67
  STAGE IA                              0                              1
  STAGE II                             17                             19
  STAGE IIA                            52                            119
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                             8                             18
  STAGE IIIA                            6                             15
  STAGE IIIB                           23                             56
  STAGE IIIC                           24                             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  38 142  24
  AMP PEAK  7(8P11.23) WILD-TYPE  16  69 271  42
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  T1                            4                             16
  T2                           38                             69
  T3                          142                            271
  T4                           24                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(8P11.23) MUTATED   118  46  43
  AMP PEAK  7(8P11.23) WILD-TYPE 224 103  71
D7V6, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  N0                          118                            224
  N1                           46                            103
  N2                           43                             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"
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED   147  31
  AMP PEAK  7(8P11.23) WILD-TYPE 301  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED    147   31
  AMP PEAK  7(8P11.23) WILD-TYPE  301   55
   clus
vv  AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  0                          147                            301
  1                           31                             55
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.23) MUTATED    95 114
  AMP PEAK  7(8P11.23) WILD-TYPE 191 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED     95  114
  AMP PEAK  7(8P11.23) WILD-TYPE  191  208
        clus
vv       AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  FEMALE                           95                            191
  MALE                            114                            208
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                    139
  AMP PEAK  7(8P11.23) WILD-TYPE                  242
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.23) MUTATED                              17
  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                            17
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  7(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      242
  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     4 205
  AMP PEAK  7(8P11.23) WILD-TYPE   5 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.23) MUTATED      4  205
  AMP PEAK  7(8P11.23) WILD-TYPE    5  394
     clus
vv    AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  NO                             4                              5
  YES                          205                            394
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.23) MUTATED   143   1  16  15
  AMP PEAK  7(8P11.23) WILD-TYPE 296   4  20  14
D7V11, multiclass
    clus
vv   AMP PEAK  7(8P11.23) MUTATED AMP PEAK  7(8P11.23) WILD-TYPE
  R0                          143                            296
  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                          19   112
  AMP PEAK  7(8P11.23) WILD-TYPE                        41   180
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     112
                                  clus
vv                                 AMP PEAK  7(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    41
  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   192  48
  AMP PEAK  8(8P11.21) WILD-TYPE 276  67
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           240                            343 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                            48                             67 
$`AMP PEAK  8(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47        11.47        43.76        43.76        43.43        24.33 
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        19.04 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3867 
       10.06        36.95        17.03         0.00        31.07        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3971 
       27.02        18.05         2.01        12.99        24.00        16.08 
TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U 
       34.06        24.00        19.00        18.05         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W 
       21.99         1.02        37.02        51.98         0.92        41.00 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
        0.07         5.79        27.42        16.44         0.92        27.09 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       21.44        17.26        32.94         5.13        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        61.41        49.41         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 
        1.94         2.24         3.06         2.14         0.07         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      102.44        15.62        49.08        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02        25.02         8.02        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       16.01        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 
       29.03        14.99        12.99        13.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 
       11.08        10.06        11.51        20.19         1.32         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04        13.41        11.38        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H 
       38.20       130.65         7.50        44.32         6.12       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
       98.24         8.61        13.64        13.45         6.18        16.31 
TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       16.24         8.35        74.56        67.30        53.62        44.68 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       45.11        39.42        26.43        46.75        47.15        18.18 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       10.98        15.65        29.46        32.98         8.42        30.28 
TCGA-WS-AB45 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 
       70.03        20.02        10.39        65.98        36.03        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3883 
       24.00         1.02         2.01         0.99        32.98         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95         1.02        48.03        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
        1.02         0.99        23.01        15.95         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       31.00        64.01        51.98         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 
        0.49         1.45         0.69         0.72         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        4.73        78.12         7.17        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 
      129.27        24.13         0.49        17.00        15.85        16.31 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       11.51        10.78        13.64        37.51        28.57        32.19 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK  8(8P11.21) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
        4.80        46.65        42.90        42.28        44.91        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        37.02        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       30.44        29.19        33.53        22.09        22.06        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       56.25         5.03         7.04         3.02        58.03        63.98 
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-3525 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 
        8.05         0.00        19.07        34.03         0.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 
       17.95        29.95        23.01        13.94        61.02         6.05 
TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3710 
        2.01         0.92        47.05        11.01        85.05        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02        14.93         0.00        10.06         0.00 
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-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       17.03        29.98        31.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
        2.01        20.98        34.03         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       13.05        26.01        25.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        38.04        30.02        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       38.04         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       22.03        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        22.42        10.88         0.20 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.85        19.33        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 
       58.39         1.41         5.65        65.00         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
      100.01        29.56         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
        0.10        17.56        40.34        70.16        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 
        2.93       124.27        23.05        26.04        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       22.03        17.03        12.00        14.04        16.04        21.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 
       45.40        12.26        19.59        13.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 
       18.25        43.27        15.12        17.85        12.49        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 
        9.44        11.64         1.51        12.00        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6703 
       35.97        60.79        95.18        13.38        11.11        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        29.59        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       19.43       107.67        28.21        82.39        23.51        65.85 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        35.93        36.72        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33         9.93        12.79        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       42.77        31.30         9.70        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        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        16.83        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        20.05        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        26.43         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                              0 
  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 
                        18.115                         19.590 
[1] "0.0 - 130.7 (18.1)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   183  70
  AMP PEAK  8(8P11.21) WILD-TYPE 259  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    183   70
  AMP PEAK  8(8P11.21) WILD-TYPE  259   92
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  COLON                           183                            259
  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      63        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         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8P11.21) MUTATED           23       34         9         0
  AMP PEAK  8(8P11.21) WILD-TYPE         31       27        18         2
D8V4, multiclass
            clus
vv           AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  STAGE I                              41                             63
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                            65                            106
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            10                             16
  STAGE IIIA                            9                             12
  STAGE IIIB                           29                             50
  STAGE IIIC                           23                             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  45 175  27
  AMP PEAK  8(8P11.21) WILD-TYPE  15  62 238  39
D8V5, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  T1                            5                             15
  T2                           45                             62
  T3                          175                            238
  T4                           27                             39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  8(8P11.21) MUTATED   142  56  53
  AMP PEAK  8(8P11.21) WILD-TYPE 200  93  61
D8V6, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  N0                          142                            200
  N1                           56                             93
  N2                           53                             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"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   177  43
  AMP PEAK  8(8P11.21) WILD-TYPE 271  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    177   43
  AMP PEAK  8(8P11.21) WILD-TYPE  271   43
   clus
vv  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  0                          177                            271
  1                           43                             43
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   111 142
  AMP PEAK  8(8P11.21) WILD-TYPE 175 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    111  142
  AMP PEAK  8(8P11.21) WILD-TYPE  175  180
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  FEMALE                          111                            175
  MALE                            142                            180
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                    163
  AMP PEAK  8(8P11.21) WILD-TYPE                  218
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                              20
  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                            20
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  8(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      218
  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     3 250
  AMP PEAK  8(8P11.21) WILD-TYPE   6 349
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED      3  250
  AMP PEAK  8(8P11.21) WILD-TYPE    6  349
     clus
vv    AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  NO                             3                              6
  YES                          250                            349
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(8P11.21) MUTATED   172   2  22  16
  AMP PEAK  8(8P11.21) WILD-TYPE 267   3  14  13
D8V11, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  R0                          172                            267
  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                          22   132
  AMP PEAK  8(8P11.21) WILD-TYPE                        38   160
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK  8(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    38
  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  62
  AMP PEAK  9(8Q12.1) WILD-TYPE 220  53
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                          310                           273 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                           62                            53 
$`AMP PEAK  9(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
       11.47        11.47        43.76        43.43        24.33        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       45.60        13.94        16.57        37.25        37.02        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-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       33.99        13.02        24.00        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 
       15.02         5.98        37.05        36.00         5.03        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 
       19.04        10.06        36.95        37.02        17.03        33.07 
TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.00         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 
       29.98        18.05         2.01        12.99        24.00        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
        2.01        16.08        34.06        26.01        24.00        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00R TCGA-AA-A00U 
       13.94        19.00        18.05        38.04         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A029 TCGA-AA-A02E 
       21.99        12.00        31.00         1.02        51.98         2.96 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 
        5.03         0.92        41.00         0.07         4.21         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       27.42         0.20        16.44         0.92        27.09        16.31 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 
        0.20        21.44        17.26        18.84        75.25        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-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 
        1.94         2.24         3.06         2.14         0.07         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      102.44        15.62        49.08        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02         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-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        13.02        11.01        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       10.06        12.26        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 
       11.38        10.26       119.70        38.20       130.65       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32         6.12        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       16.31        16.24         8.35        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       35.93        36.00        26.43        46.75        47.15        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       10.98         9.93        15.65        29.46        32.98         8.42 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       12.72        37.74        10.39        20.02        10.39        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02        36.03        24.00         1.02        46.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
        6.05         0.99        19.99         7.99         1.02        32.98 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
        1.02        36.95         1.02        48.03        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         1.02        17.03         0.99        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       64.01        51.98         1.94        61.97        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        1.45         0.69         0.72        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        4.73        78.12         7.17        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00        10.98        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 
       41.36        57.24        24.13         0.49        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       16.34        16.31        11.51        10.78        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       37.51        28.57         0.39        32.19         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  9(8Q12.1) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
        4.80        43.76        46.65        42.90        42.28        44.91 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       37.05        34.65        14.53        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       22.09        22.06        22.52         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       24.39        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       56.25         7.04         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 
       23.01        19.99        13.94        61.02         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       47.05        11.01        19.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 
       14.93         0.00        10.06         0.00        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.07        53.00        31.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
        2.01        20.98        21.99        50.99        13.05        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
       19.07         7.96        27.02        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        39.98         2.01        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       40.96        21.37        56.55         0.79         0.72        22.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
       10.88         0.46        14.50         0.95        15.75        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33        50.37        58.39         1.41         5.65 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        6.77       100.01         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
        0.10        17.56        40.34        70.16        21.99        21.14 
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-6674 TCGA-CM-6675 TCGA-CM-6678 
       16.04        15.02        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       12.03        45.40        19.59        20.42        17.75        18.25 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       17.85        12.49        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       12.00        24.43        92.75        49.91        13.32        12.59 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 
       81.37       119.93        95.18        11.11        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
      107.67        28.21        82.39        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33        12.79        13.05        12.00        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 
       31.30         9.70        13.55        19.10        14.50        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       15.39        86.63        11.84        12.00         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
       20.05        34.03         2.01        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99         0.99        29.98         0.99         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-4001 
       17.03        13.02        35.01        14.01        19.99        36.03 
TCGA-AG-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-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       49.97        38.96        41.00        26.43         1.81         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6160 
        6.97        13.97        10.98        11.01        15.02        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       12.95         5.29       129.27        51.48        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       20.55        19.96        20.91        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 
        8.61        17.46        11.97         8.45        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.69         0.53         1.12 

  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE 
                        18.05                         19.66 
[1] "0.0 - 140.4 (18.1)" "0.0 - 139.2 (19.7)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   233  93
  AMP PEAK  9(8Q12.1) WILD-TYPE 209  69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    233   93
  AMP PEAK  9(8Q12.1) WILD-TYPE  209   69
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON                          233                           209
  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      56        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         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q12.1) MUTATED           33       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                            56
  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                            36
  STAGE IIIC                          33                            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  54 228  36
  AMP PEAK  9(8Q12.1) WILD-TYPE  13  53 185  30
D9V5, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  T1                           7                            13
  T2                          54                            53
  T3                         228                           185
  T4                          36                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  9(8Q12.1) MUTATED   174  78  71
  AMP PEAK  9(8Q12.1) WILD-TYPE 168  71  43
D9V6, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  N0                         174                           168
  N1                          78                            71
  N2                          71                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   226  57
  AMP PEAK  9(8Q12.1) WILD-TYPE 222  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    226   57
  AMP PEAK  9(8Q12.1) WILD-TYPE  222   29
   clus
vv  AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  0                         226                           222
  1                          57                            29
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(8Q12.1) MUTATED   148 178
  AMP PEAK  9(8Q12.1) WILD-TYPE 138 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED    148  178
  AMP PEAK  9(8Q12.1) WILD-TYPE  138  144
        clus
vv       AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  FEMALE                         148                           138
  MALE                           178                           144
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                    209
  AMP PEAK  9(8Q12.1) WILD-TYPE                  172
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q12.1) MUTATED                              24
  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                           24
  RECTAL ADENOCARCINOMA                                   87
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  9(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     172
  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     8 318
  AMP PEAK  9(8Q12.1) WILD-TYPE   1 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(8Q12.1) MUTATED      8  318
  AMP PEAK  9(8Q12.1) WILD-TYPE    1  281
     clus
vv    AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  NO                            8                             1
  YES                         318                           281
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(8Q12.1) MUTATED   225   3  26  17
  AMP PEAK  9(8Q12.1) WILD-TYPE 214   2  10  12
D9V11, multiclass
    clus
vv   AMP PEAK  9(8Q12.1) MUTATED AMP PEAK  9(8Q12.1) WILD-TYPE
  R0                         225                           214
  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                          32   169
  AMP PEAK  9(8Q12.1) WILD-TYPE                        28   123
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK  9(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  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  71
  AMP PEAK 10(8Q24.21) WILD-TYPE 192  44
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                           347                            236 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                            71                             44 
$`AMP PEAK 10(8Q24.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47        11.47        43.76        43.76        43.43        24.33 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 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 
       56.25         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-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        0.00        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 
       14.01        33.99        13.02        24.00        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       50.04        47.01        15.02         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 
        5.03        85.05        19.04        19.04        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-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-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 
       16.08        34.06        26.01        24.00        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 
       19.00        18.05         0.99        17.03        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
       10.98        12.00        31.00         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
        2.96         2.01         5.03         0.92        41.00         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       21.37         4.21         5.79        22.42        27.42         0.20 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
       16.44         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       17.26        18.84        75.25         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-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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 
        2.24         3.06         2.14         3.29         0.07         0.10 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1.35       102.44        15.62        49.08        51.32        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
        2.01        20.02        37.02        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 
       29.03        21.99        14.99        12.99        13.02        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 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-A0XD 
        9.04        13.41        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       38.20       130.65        49.91       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        67.30        65.85        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-A6GB 
       26.43        46.75        47.15        18.18        10.98        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
       12.00        29.46        32.98         8.42        30.28        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        39.48        17.23        43.04        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        20.02        10.39        86.63        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02        36.03        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
        2.01        50.04         6.05         0.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
        0.99         1.02        32.98         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       17.03         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         0.99        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        37.02        15.95         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       70.03        64.01        51.98         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.04         0.49         1.45         0.69         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         9.37         4.73        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 
       24.13        32.61         0.49         2.40        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       16.34        16.31        11.51        10.78        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       37.51        28.57         0.39        32.19         0.53         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 10(8Q24.21) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
        4.80        46.65        42.90        42.28        44.91        37.05 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       14.53        30.44        33.53        22.09        22.06        22.52 
TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       24.92        61.84         7.04         3.02        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 
       13.02        38.99         1.02         9.07        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 
       19.07        34.03        21.01        17.95        29.95        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       13.94        61.02         2.01         0.92        47.05        11.01 
TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.00        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        14.93         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00        32.05        31.07        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       26.01        24.00         2.01        21.99        50.99        13.05 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07         7.96        27.02        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       14.99        34.98        15.02        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02        35.01        33.04        35.01        26.01        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       39.98        22.03        39.98        18.05        40.96        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 
        0.79         0.72        10.88         0.46        14.50         0.95 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       15.75        17.82        17.85        19.33        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        1.41         6.77       100.01         3.25         0.26         0.33 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       17.56        40.34        70.16        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 
       23.05        26.04        22.03        12.00        16.04        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 
       12.03        45.40        20.42        17.75        18.25        17.85 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 
       12.39         9.44        11.64         1.51        12.00        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 
       14.04        26.47        81.37       119.93        95.18        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        29.59        33.67        13.25         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-A6GA TCGA-NH-A6GC 
       91.79        52.80        19.33        19.33         9.93        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-4110 
       13.05        42.77        31.30         9.70        19.10        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       16.83        15.39        11.84        12.00         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3728 
       20.05        34.03        12.03        15.95        19.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 
        0.99        19.99        13.02        35.01        14.01        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 
       13.94         6.02        36.03        12.00        10.98        49.97 
TCGA-AG-A02G TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
       38.96        26.43         1.81         6.05         6.97        13.97 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG 
       15.02        30.05        12.95         5.29       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       20.55        19.96        20.91        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 
        8.61        17.46        11.97         8.45        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6861 
        0.69         1.12 

  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                             0                              0 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE 
                         18.84                          19.33 
[1] "0.0 - 140.4 (18.8)" "0.0 - 139.2 (19.3)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   255 107
  AMP PEAK 10(8Q24.21) WILD-TYPE 187  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    255  107
  AMP PEAK 10(8Q24.21) WILD-TYPE  187   55
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON                           255                            187
  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      48        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         32
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(8Q24.21) MUTATED           34       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                             48
  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                             32
  STAGE IIIC                           34                             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  64 253  37
  AMP PEAK 10(8Q24.21) WILD-TYPE  12  43 160  29
D10V5, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  T1                            8                             12
  T2                           64                             43
  T3                          253                            160
  T4                           37                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 10(8Q24.21) MUTATED   198  85  77
  AMP PEAK 10(8Q24.21) WILD-TYPE 144  64  37
D10V6, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  N0                          198                            144
  N1                           85                             64
  N2                           77                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   257  62
  AMP PEAK 10(8Q24.21) WILD-TYPE 191  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    257   62
  AMP PEAK 10(8Q24.21) WILD-TYPE  191   24
   clus
vv  AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  0                          257                            191
  1                           62                             24
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(8Q24.21) MUTATED   163 200
  AMP PEAK 10(8Q24.21) WILD-TYPE 123 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED    163  200
  AMP PEAK 10(8Q24.21) WILD-TYPE  123  122
        clus
vv       AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  FEMALE                          163                            123
  MALE                            200                            122
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                    225
  AMP PEAK 10(8Q24.21) WILD-TYPE                  156
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(8Q24.21) MUTATED                              29
  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                            29
  RECTAL ADENOCARCINOMA                                   100
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 10(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      156
  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     8 355
  AMP PEAK 10(8Q24.21) WILD-TYPE   1 244
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(8Q24.21) MUTATED      8  355
  AMP PEAK 10(8Q24.21) WILD-TYPE    1  244
     clus
vv    AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  NO                             8                              1
  YES                          355                            244
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(8Q24.21) MUTATED   253   3  27  19
  AMP PEAK 10(8Q24.21) WILD-TYPE 186   2   9  10
D10V11, multiclass
    clus
vv   AMP PEAK 10(8Q24.21) MUTATED AMP PEAK 10(8Q24.21) WILD-TYPE
  R0                          253                            186
  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                          35   184
  AMP PEAK 10(8Q24.21) WILD-TYPE                        25   108
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     184
                                  clus
vv                                 AMP PEAK 10(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    25
  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    28   8
  AMP PEAK 11(10Q22.3) WILD-TYPE 440 107
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                            36                            547 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                             8                            107 
$`AMP PEAK 11(10Q22.3) MUTATED`
TCGA-4T-AA8H TCGA-A6-6649 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3952 
       11.47        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        17.26        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-QL-A97D TCGA-AF-2689 TCGA-AF-A56K TCGA-AG-3587 TCGA-AG-3598 
       36.00         9.70        39.48        86.63        46.03        50.04 
TCGA-AG-3999 TCGA-AG-A01W TCGA-AG-A020 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-4745 
       28.04        70.03        10.98        10.19         6.05        10.98 

$`AMP PEAK 11(10Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-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-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-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        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        24.03        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-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-3986 
       13.05        34.06        26.01        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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         5.79        22.42        27.42        10.88         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
        0.95        15.75         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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        49.08        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 
       25.02        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        45.40        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        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 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 
       13.25         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        67.30        65.85        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        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       19.33        19.33         9.93        15.65        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        70.03        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        12.72        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       15.39        20.02        10.39        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02        34.03         2.01        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-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-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-4001 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        31.00        64.01        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-CI-6620 
        1.45         0.69         0.72        26.43         1.81         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        78.12         7.17 
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        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-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 
       28.57         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                          1.02                           0.00 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE 
                        16.635                         19.070 
[1] "1.0 - 140.4 (16.6)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    28  11
  AMP PEAK 11(10Q22.3) WILD-TYPE 414 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     28   11
  AMP PEAK 11(10Q22.3) WILD-TYPE  414  151
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON                            28                            414
  RECTUM                           11                            151
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(10Q22.3) MUTATED         5        0        2         9         0
  AMP PEAK 11(10Q22.3) WILD-TYPE      99        1       34       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         75
                                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         48       56        26         2
D11V4, multiclass
            clus
vv           AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              2                             34
  STAGE IIA                             9                            162
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            2                             19
  STAGE IIIB                            4                             75
  STAGE IIIC                            6                             48
  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   4  32   2
  AMP PEAK 11(10Q22.3) WILD-TYPE  19 103 381  64
D11V5, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  T1                            1                             19
  T2                            4                            103
  T3                           32                            381
  T4                            2                             64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 11(10Q22.3) MUTATED    16  11  12
  AMP PEAK 11(10Q22.3) WILD-TYPE 326 138 102
D11V6, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  N0                           16                            326
  N1                           11                            138
  N2                           12                            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    27   6
  AMP PEAK 11(10Q22.3) WILD-TYPE 421  80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     27    6
  AMP PEAK 11(10Q22.3) WILD-TYPE  421   80
   clus
vv  AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  0                           27                            421
  1                            6                             80
[1] 2 2
[1] FALSE
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED    17  22
  AMP PEAK 11(10Q22.3) WILD-TYPE 269 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED     17   22
  AMP PEAK 11(10Q22.3) WILD-TYPE  269  300
        clus
vv       AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  FEMALE                           17                            269
  MALE                             22                            300
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                     24
  AMP PEAK 11(10Q22.3) WILD-TYPE                  357
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                               4
  AMP PEAK 11(10Q22.3) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                       9
  AMP PEAK 11(10Q22.3) WILD-TYPE                   137
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(10Q22.3) MUTATED                                1
  AMP PEAK 11(10Q22.3) WILD-TYPE                             12
D11V9, multiclass
                                clus
vv                               AMP PEAK 11(10Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     24
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 11(10Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      357
  COLON MUCINOUS ADENOCARCINOMA                              56
  RECTAL ADENOCARCINOMA                                     137
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                                cls
clus                               0   1
  AMP PEAK 11(10Q22.3) MUTATED     1  38
  AMP PEAK 11(10Q22.3) WILD-TYPE   8 561
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(10Q22.3) MUTATED      1   38
  AMP PEAK 11(10Q22.3) WILD-TYPE    8  561
     clus
vv    AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  NO                             1                              8
  YES                           38                            561
[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 413   5  35  28
D11V11, multiclass
    clus
vv   AMP PEAK 11(10Q22.3) MUTATED AMP PEAK 11(10Q22.3) WILD-TYPE
  R0                           26                            413
  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                           4    21
  AMP PEAK 11(10Q22.3) WILD-TYPE                        56   271
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(10Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      21
                                  clus
vv                                 AMP PEAK 11(10Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    56
  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  26
  AMP PEAK 12(11P15.5) WILD-TYPE 364  89
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                           130                            453 
  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE 
                            26                             89 
$`AMP PEAK 12(11P15.5) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
       43.76        43.43        24.33        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3506 
       25.18        23.87         9.63         5.03         1.02        58.03 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        9.07        24.03         0.00        19.07        34.03        29.00 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 
       12.99        13.02        24.00        23.01        13.94        19.99 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 
       50.04        47.01         5.03        25.02        17.98        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 
       17.03        33.07         0.99        24.03        18.05        20.98 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01D 
       27.02        19.07        34.03        17.03        21.99        10.98 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6888 
        1.02        35.01        26.01        39.98         5.03         4.21 
TCGA-AD-6901 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 
       22.42         0.46        16.31         0.95        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 
       62.79        29.56         3.19         1.94         2.14         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 
        0.26         1.35       102.44         8.02        30.08        17.03 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 
       29.03        21.99        11.08        12.26        13.51         1.32 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G 
       17.85         7.53        13.41        49.91        35.97        60.79 
TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 
       13.38        13.64         8.35        74.56        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6314 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2689 
       45.11        35.93        42.77        29.46        30.28        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       17.23        13.55        10.39        16.83        20.02        10.39 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3587 
       65.98        36.03        12.00         8.02        20.05        46.03 
TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3894 TCGA-AG-4001 
       34.03        19.99        19.99         0.99        14.01        36.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 
        1.02        25.97        31.00        26.43        10.19         9.37 
TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       13.97        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 
       30.05       126.44         0.49         2.40        20.55        16.31 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 TCGA-G5-6233 
        0.39        32.19         1.12        18.28 

$`AMP PEAK 12(11P15.5) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        35.11        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 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-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        24.16        20.61        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       56.25         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 
       37.05        36.03         8.05        19.07        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        21.01        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-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       11.01         5.98        37.05        19.00        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        19.04        10.06        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 
        1.02        15.95        38.99        36.95        14.93         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       10.06         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        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-3989 
       13.05        34.06        26.01        25.02        24.00         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        38.04         4.01        27.02        42.02         0.99 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       31.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O 
       37.02        39.06        51.98         2.96         2.01         0.92 
TCGA-AA-A02R TCGA-AA-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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20        16.44         0.92        14.50        27.09 
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        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10       100.01         5.23        11.74         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.06         3.25         3.29         0.33         0.10        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        49.08        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        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        12.00        14.04        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
      119.93       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21        82.39        23.51        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        51.75        39.42        36.72        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       46.75        47.15        52.80        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        13.05        12.00 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30         9.70        70.03        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        36.03        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        78.12         7.17        10.98        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        10.98        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 
       28.57         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                              0 
  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 
                         19.53                          19.04 
[1] "0.0 - 126.4 (19.5)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    90  44
  AMP PEAK 12(11P15.5) WILD-TYPE 352 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     90   44
  AMP PEAK 12(11P15.5) WILD-TYPE  352  118
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  COLON                            90                            352
  RECTUM                           44                            118
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(11P15.5) MUTATED        20        0        6        35         2
  AMP PEAK 12(11P15.5) WILD-TYPE      84        1       30       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         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(11P15.5) MUTATED           15       18         7         0
  AMP PEAK 12(11P15.5) WILD-TYPE         39       43        20         2
D12V4, multiclass
            clus
vv           AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            35                            136
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            7                             14
  STAGE IIIB                           17                             62
  STAGE IIIC                           15                             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  97   9
  AMP PEAK 12(11P15.5) WILD-TYPE  14  83 316  57
D12V5, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  T1                            6                             14
  T2                           24                             83
  T3                           97                            316
  T4                            9                             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 12(11P15.5) MUTATED    70  34  31
  AMP PEAK 12(11P15.5) WILD-TYPE 272 115  83
D12V6, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  N0                           70                            272
  N1                           34                            115
  N2                           31                             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"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    99  24
  AMP PEAK 12(11P15.5) WILD-TYPE 349  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     99   24
  AMP PEAK 12(11P15.5) WILD-TYPE  349   62
   clus
vv  AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  0                           99                            349
  1                           24                             62
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(11P15.5) MUTATED    66  70
  AMP PEAK 12(11P15.5) WILD-TYPE 220 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED     66   70
  AMP PEAK 12(11P15.5) WILD-TYPE  220  252
        clus
vv       AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  FEMALE                           66                            220
  MALE                             70                            252
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                     85
  AMP PEAK 12(11P15.5) WILD-TYPE                  296
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                               4
  AMP PEAK 12(11P15.5) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                      43
  AMP PEAK 12(11P15.5) WILD-TYPE                   103
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(11P15.5) MUTATED                                1
  AMP PEAK 12(11P15.5) WILD-TYPE                             12
D12V9, multiclass
                                clus
vv                               AMP PEAK 12(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                     85
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 12(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                      296
  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     4 132
  AMP PEAK 12(11P15.5) WILD-TYPE   5 467
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(11P15.5) MUTATED      4  132
  AMP PEAK 12(11P15.5) WILD-TYPE    5  467
     clus
vv    AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  NO                             4                              5
  YES                          132                            467
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(11P15.5) MUTATED    97   1  10   7
  AMP PEAK 12(11P15.5) WILD-TYPE 342   4  26  22
D12V11, multiclass
    clus
vv   AMP PEAK 12(11P15.5) MUTATED AMP PEAK 12(11P15.5) WILD-TYPE
  R0                           97                            342
  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                          11    64
  AMP PEAK 12(11P15.5) WILD-TYPE                        49   228
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      64
                                  clus
vv                                 AMP PEAK 12(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    49
  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   109  32
  AMP PEAK 13(12P13.32) WILD-TYPE 359  83
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                            141                             442 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                             32                              83 
$`AMP PEAK 13(12P13.32) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 
       11.47        11.47        44.91        13.94        37.02        34.65 
TCGA-A6-4105 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 
       14.53        22.09        25.08        20.61        20.12        20.28 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3529 TCGA-AA-3532 
       24.92         1.02        58.03        36.03         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 
       29.00        12.99        19.99        78.08         0.92        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 
        0.99        37.02        14.93         0.00        33.07         0.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A00F 
       12.99        24.00        26.01        24.00         2.01        34.03 
TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O 
       18.05        12.00        31.00        33.04        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6965 
       22.03        39.98        40.96         0.07        27.42         0.20 
TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 
        0.92        18.84         1.41         5.13        49.41         6.77 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 
       11.74         3.19         1.94         3.06       102.44        40.34 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 
       15.62        51.32        20.02        25.02        30.08        16.01 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       15.02        15.02        21.99        13.02        14.04        11.01 
TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 
       11.01        20.19        17.75         4.80        12.49        15.58 
TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30        11.64        13.41        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 
       24.43        13.32        44.32        95.18         8.61        35.87 
TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U 
       16.31        44.68        35.93        13.78        47.15        10.98 
TCGA-NH-A6GB TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       15.65         9.70        19.10        12.72        37.74        14.50 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 
       16.83        10.39        36.03        46.03         2.01         6.05 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
       19.99         7.99         1.02         1.02        36.95         1.02 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N 
       36.03         0.99        15.95        36.03        38.96        61.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        4.73        78.12        13.05        10.06         5.29       126.44 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 
       32.61        19.96        18.28        17.69        13.64        11.97 
TCGA-F5-6812 TCGA-G5-6233 TCGA-G5-6641 
        0.66        18.28        26.43 

$`AMP PEAK 13(12P13.32) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 
       24.33        42.28        35.11        45.60        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.25        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        23.61        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.69        24.39        23.87        19.66        16.24 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 
        8.05        19.07        19.07        34.03        26.01         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-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
        6.05         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.05        47.01        15.02        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       38.99        36.95        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
       15.02        15.02        10.98        32.02        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-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       39.06         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03F TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        5.79        22.42        10.88        16.44         0.46        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-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        12.10       100.01        29.56         5.23 
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-CA-6719 TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 
        0.33         0.10         1.35        17.56        70.16        49.08 
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-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       22.03        22.98        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       15.02        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        16.14         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04         9.44         1.51        11.38        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        49.91        12.59       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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       13.38        11.11        13.64        13.45         6.18         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         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-G4-6307 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       26.04        35.80        26.17        91.79        46.75        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
       18.18        19.33        19.33         9.93        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       13.55        10.39        15.39        20.02        86.63        65.98 
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        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       20.05        24.00         1.02        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
        0.99        15.95        19.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        19.99        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       14.01        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02         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-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 
       26.43         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        9.37        13.97         7.17        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        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       30.05        12.95        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-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57         0.39        32.19         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 

  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                              0                               0 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         126.44                          140.38 
  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE 
                         16.830                          19.825 
[1] "0.0 - 126.4 (16.8)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.4"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   110  38
  AMP PEAK 13(12P13.32) WILD-TYPE 332 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    110   38
  AMP PEAK 13(12P13.32) WILD-TYPE  332  124
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  COLON                            110                             332
  RECTUM                            38                             124
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(12P13.32) MUTATED        23        1       13        50         2
  AMP PEAK 13(12P13.32) WILD-TYPE      81        0       23       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         70
                                 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         40       46        19         2
D13V4, multiclass
            clus
vv           AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  STAGE I                               23                              81
  STAGE IA                               1                               0
  STAGE II                              13                              23
  STAGE IIA                             50                             121
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              5                              21
  STAGE IIIA                             7                              14
  STAGE IIIB                             9                              70
  STAGE IIIC                            14                              40
  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  28 100  19
  AMP PEAK 13(12P13.32) WILD-TYPE  18  79 313  47
D13V5, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  T1                             2                              18
  T2                            28                              79
  T3                           100                             313
  T4                            19                              47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 13(12P13.32) MUTATED    94  27  29
  AMP PEAK 13(12P13.32) WILD-TYPE 248 122  85
D13V6, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  N0                            94                             248
  N1                            27                             122
  N2                            29                              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"
D13V7, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED   107  20
  AMP PEAK 13(12P13.32) WILD-TYPE 341  66
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED    107   20
  AMP PEAK 13(12P13.32) WILD-TYPE  341   66
   clus
vv  AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  0                           107                             341
  1                            20                              66
[1] 2 2
[1] FALSE
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED    69  81
  AMP PEAK 13(12P13.32) WILD-TYPE 217 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED     69   81
  AMP PEAK 13(12P13.32) WILD-TYPE  217  241
        clus
vv       AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  FEMALE                            69                             217
  MALE                              81                             241
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                     97
  AMP PEAK 13(12P13.32) WILD-TYPE                  284
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                              13
  AMP PEAK 13(12P13.32) WILD-TYPE                            47
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                      32
  AMP PEAK 13(12P13.32) WILD-TYPE                   114
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12P13.32) MUTATED                                5
  AMP PEAK 13(12P13.32) WILD-TYPE                              8
D13V9, multiclass
                                clus
vv                               AMP PEAK 13(12P13.32) MUTATED
  COLON ADENOCARCINOMA                                      97
  COLON MUCINOUS ADENOCARCINOMA                             13
  RECTAL ADENOCARCINOMA                                     32
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 13(12P13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       284
  COLON MUCINOUS ADENOCARCINOMA                               47
  RECTAL ADENOCARCINOMA                                      114
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                                 cls
clus                                0   1
  AMP PEAK 13(12P13.32) MUTATED     3 147
  AMP PEAK 13(12P13.32) WILD-TYPE   6 452
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(12P13.32) MUTATED      3  147
  AMP PEAK 13(12P13.32) WILD-TYPE    6  452
     clus
vv    AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  NO                              3                               6
  YES                           147                             452
[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 330   4  30  23
D13V11, multiclass
    clus
vv   AMP PEAK 13(12P13.32) MUTATED AMP PEAK 13(12P13.32) WILD-TYPE
  R0                           109                             330
  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                          12    74
  AMP PEAK 13(12P13.32) WILD-TYPE                        48   218
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       74
                                  clus
vv                                 AMP PEAK 13(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     48
  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   303  75
  AMP PEAK 14(13Q12.13) WILD-TYPE 165  40
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                            378                             205 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                             75                              40 
$`AMP PEAK 14(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.57        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        33.53        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 
       56.25         9.63         5.03         7.04        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       58.03         6.97        38.99         9.07        24.03        36.03 
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-3558 
       14.01        33.99        21.01        13.02        24.00        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       19.99        13.94        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        15.02         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.03        85.05        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       25.02        36.95        37.02        14.93        17.03        10.06 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       27.02        29.98         2.01        12.99        24.00        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       27.02        13.94        19.00        34.03        38.04        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
       31.00        33.04         2.96        39.98         2.01        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        40.96        21.37         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        16.44        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       15.75        21.44        17.26        18.84        75.25        50.37 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        2.24         3.06         0.07         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
       49.08        21.99         2.01        20.02        25.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        10.06        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        17.75        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       10.13        12.43        14.30         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        10.26       119.70       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 
       13.32         7.50       131.51         7.76         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       26.47       119.93        35.97         8.61        13.38         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       65.85        44.68        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        35.80        91.79        46.75        47.15        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42         9.70        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        13.55        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       14.50        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        11.84         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
       46.03        34.03         2.01         0.99        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99        29.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07        12.00        51.98        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04         0.49         0.69         0.72        26.43         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        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        10.98        30.05        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        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 
       42.90        24.33        37.05        37.25        37.02        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
        0.00        19.07        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        47.01        11.01 
TCGA-AA-3692 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       36.00        26.99        19.04         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       38.99         0.00         0.00        33.07         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 
       53.00        18.05        31.00        33.01        24.00         2.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
        2.01        25.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 
        4.01        27.02         0.99        17.03        21.99        34.98 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02        39.06        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       22.03        18.05         0.07         4.21        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 
       10.88         0.46         0.92        27.09         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 
       17.85        19.33        58.39         5.65        32.94        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01         3.19         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.26         0.33         0.10        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       51.32        21.14         2.93       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 
       26.04        27.02        15.02        15.02        12.00        21.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 
       14.04        12.95        13.05        12.03        45.40        20.19 
TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       20.42        16.14        15.58        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
        1.51        24.43        38.20        12.59       140.38        44.32 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      135.65       139.17        81.37        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
       95.18        11.11        13.64        13.45        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       16.31        19.43        67.30        53.62        55.04        51.75 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 
       36.72        22.09        26.04        13.78        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 
       10.98        19.33         9.93        12.79        31.30        70.03 
TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 
       12.72        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-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6681 
       41.00         1.45         1.81        10.19        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 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE 
                          19.02                           19.33 
[1] "0.1 - 131.5 (19.0)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   269 123
  AMP PEAK 14(13Q12.13) WILD-TYPE 173  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    269  123
  AMP PEAK 14(13Q12.13) WILD-TYPE  173   39
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  COLON                            269                             173
  RECTUM                           123                              39
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(13Q12.13) MUTATED        64        0       16        98         4
  AMP PEAK 14(13Q12.13) WILD-TYPE      40        1       20        73         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(13Q12.13) MUTATED           3        15         17         59
  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           39       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                               64                              40
  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                            59                              20
  STAGE IIIC                            39                              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  65 272  44
  AMP PEAK 14(13Q12.13) WILD-TYPE   6  42 141  22
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  T1                            14                               6
  T2                            65                              42
  T3                           272                             141
  T4                            44                              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   195 113  86
  AMP PEAK 14(13Q12.13) WILD-TYPE 147  36  28
D14V6, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  N0                           195                             147
  N1                           113                              36
  N2                            86                              28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   280  69
  AMP PEAK 14(13Q12.13) WILD-TYPE 168  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    280   69
  AMP PEAK 14(13Q12.13) WILD-TYPE  168   17
   clus
vv  AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  0                           280                             168
  1                            69                              17
[1] 2 2
[1] FALSE
D14V8, binary
                                 cls
clus                                0   1
  AMP PEAK 14(13Q12.13) MUTATED   183 213
  AMP PEAK 14(13Q12.13) WILD-TYPE 103 109
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED    183  213
  AMP PEAK 14(13Q12.13) WILD-TYPE  103  109
        clus
vv       AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  FEMALE                           183                             103
  MALE                             213                             109
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                    251
  AMP PEAK 14(13Q12.13) WILD-TYPE                  130
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                              18
  AMP PEAK 14(13Q12.13) WILD-TYPE                            42
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                     117
  AMP PEAK 14(13Q12.13) WILD-TYPE                    29
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.13) MUTATED                                5
  AMP PEAK 14(13Q12.13) WILD-TYPE                              8
D14V9, multiclass
                                clus
vv                               AMP PEAK 14(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                     251
  COLON MUCINOUS ADENOCARCINOMA                             18
  RECTAL ADENOCARCINOMA                                    117
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 14(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                       130
  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     7 389
  AMP PEAK 14(13Q12.13) WILD-TYPE   2 210
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 14(13Q12.13) MUTATED      7  389
  AMP PEAK 14(13Q12.13) WILD-TYPE    2  210
     clus
vv    AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  NO                              7                               2
  YES                           389                             210
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 14(13Q12.13) MUTATED   281   3  28  13
  AMP PEAK 14(13Q12.13) WILD-TYPE 158   2   8  16
D14V11, multiclass
    clus
vv   AMP PEAK 14(13Q12.13) MUTATED AMP PEAK 14(13Q12.13) WILD-TYPE
  R0                           281                             158
  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                          39   204
  AMP PEAK 14(13Q12.13) WILD-TYPE                        21    88
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      204
                                  clus
vv                                 AMP PEAK 14(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     21
  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   300  73
  AMP PEAK 15(13Q12.2) WILD-TYPE 168  42
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                           373                            210 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                            73                             42 
$`AMP PEAK 15(13Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.57        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        33.53        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 
       56.25         9.63         5.03         7.04        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       58.03         6.97        38.99         9.07        24.03        36.03 
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-3558 
       14.01        33.99        21.01        13.02        24.00        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       19.99        13.94        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        15.02         5.98        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
       85.05        19.04        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        12.99        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-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-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        38.04        42.02        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E 
       10.98        32.02        12.00        31.00        33.04         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 
       39.98         2.01        41.00        39.98        40.96        21.37 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         5.79        22.42        27.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L 
       14.50        16.31         0.95        15.75        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       18.84        75.25        50.37         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 
        5.23        11.74         1.94         2.24         3.06         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        1.35        17.56       102.44        49.08        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        16.01         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       10.06        12.26        19.59        13.51        11.51        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       17.13        12.49         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32         7.50       131.51 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
        7.76         6.12        14.04        26.47       119.93        35.97 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        8.61        13.38         6.18        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       13.25         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       82.39        23.51        65.85        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-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       47.15        18.18        19.33        15.65        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42         9.70        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       86.63        65.98        11.84         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 
        1.02        46.03        34.03         2.01         0.99        19.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       19.99         0.99        29.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       36.95        17.03        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        0.99         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       36.03         9.07        12.00        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       26.43         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 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.00        15.02        36.00        10.98        30.05        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       16.41        11.51        10.78        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       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 
       42.90        24.33        37.05        37.25        37.02        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
        0.00        19.07        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        47.01        11.01 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 
       36.00         5.03        26.99        19.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 
       17.98        15.95        38.99         0.00         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
        0.00        36.03        53.00        18.05        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A 
       24.00         2.01         2.01        25.02        24.00        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       17.03        21.99        34.98        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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 
       51.98         5.03         0.92        22.03        18.05         0.07 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        4.21        56.55         0.72        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       27.09         0.20        17.82        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 
        5.65        32.94        61.41         6.77       100.01         3.19 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29         0.26         0.33         0.10 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        70.16        15.62        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        27.02        15.02 
TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       15.02        12.00        21.99        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.03        45.40        20.19        20.42        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.39         9.44        11.64         1.51        24.43        38.20 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38        44.32       135.65       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 
       13.45        35.87         1.55        16.31        19.43        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       67.30        53.62        55.04        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        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 
        9.93        12.79        31.30        70.03        12.72        16.83 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3598 
       36.03        12.00        32.02         8.02        24.00        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       12.03         6.05        15.95         7.99         1.02        32.98 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J 
        0.99        13.02        48.03        20.98        13.94         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6547 
       31.00        70.03        64.01        10.98        61.97         1.45 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 
        1.81        10.19         6.05        13.97        12.95         5.29 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 
       19.96         8.61        13.64        17.46         0.53         1.12 

  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE 
                         19.04                          19.20 
[1] "0.1 - 131.5 (19.0)" "0.0 - 140.4 (19.2)"
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   265 122
  AMP PEAK 15(13Q12.2) WILD-TYPE 177  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    265  122
  AMP PEAK 15(13Q12.2) WILD-TYPE  177   40
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  COLON                           265                            177
  RECTUM                          122                             40
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(13Q12.2) MUTATED        64        0       16        96         4
  AMP PEAK 15(13Q12.2) WILD-TYPE      40        1       20        75         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(13Q12.2) MUTATED           3        15         17         59
  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           38       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                              64                             40
  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                           59                             20
  STAGE IIIC                           38                             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  65 267  44
  AMP PEAK 15(13Q12.2) WILD-TYPE   6  42 146  22
D15V5, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  T1                           14                              6
  T2                           65                             42
  T3                          267                            146
  T4                           44                             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   193 111  85
  AMP PEAK 15(13Q12.2) WILD-TYPE 149  38  29
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  N0                          193                            149
  N1                          111                             38
  N2                           85                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   277  67
  AMP PEAK 15(13Q12.2) WILD-TYPE 171  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    277   67
  AMP PEAK 15(13Q12.2) WILD-TYPE  171   19
   clus
vv  AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  0                          277                            171
  1                           67                             19
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q12.2) MUTATED   179 212
  AMP PEAK 15(13Q12.2) WILD-TYPE 107 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED    179  212
  AMP PEAK 15(13Q12.2) WILD-TYPE  107  110
        clus
vv       AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  FEMALE                          179                            107
  MALE                            212                            110
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                    247
  AMP PEAK 15(13Q12.2) WILD-TYPE                  134
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                              18
  AMP PEAK 15(13Q12.2) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                     116
  AMP PEAK 15(13Q12.2) WILD-TYPE                    30
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q12.2) MUTATED                                5
  AMP PEAK 15(13Q12.2) WILD-TYPE                              8
D15V9, multiclass
                                clus
vv                               AMP PEAK 15(13Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    247
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                   116
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 15(13Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      134
  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     7 384
  AMP PEAK 15(13Q12.2) WILD-TYPE   2 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q12.2) MUTATED      7  384
  AMP PEAK 15(13Q12.2) WILD-TYPE    2  215
     clus
vv    AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  NO                             7                              2
  YES                          384                            215
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(13Q12.2) MUTATED   278   3  27  13
  AMP PEAK 15(13Q12.2) WILD-TYPE 161   2   9  16
D15V11, multiclass
    clus
vv   AMP PEAK 15(13Q12.2) MUTATED AMP PEAK 15(13Q12.2) WILD-TYPE
  R0                          278                            161
  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                          39   201
  AMP PEAK 15(13Q12.2) WILD-TYPE                        21    91
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 15(13Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    21
  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   302  75
  AMP PEAK 16(13Q22.1) WILD-TYPE 166  40
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                           377                            206 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                            75                             40 
$`AMP PEAK 16(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.43        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.57        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        33.53        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 
       56.25         9.63         5.03         7.04        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       58.03         6.97        38.99         9.07        24.03        36.03 
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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 
       14.01        21.01        13.02        24.00        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 
       13.94        19.99        78.08         6.05        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        15.02         5.98        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
       85.05        19.04        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 
        2.01        12.99        24.00        26.01         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-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       26.01        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        34.03        38.04        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
        1.02        33.04         2.96        39.98         2.01        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         5.79        22.42        27.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L 
       14.50        16.31         0.95        15.75        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       18.84        75.25        50.37         1.41         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-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        49.08        21.99         2.01        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        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        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         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-A0XD 
       13.41        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       38.20       130.65        92.75        49.91        13.32         7.50 
TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51         7.76         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.97        13.38         6.18        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       13.25         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 
       82.39        23.51        74.56        65.85        44.68        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 
       39.42        35.93        36.00        26.43        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB 
       46.75        47.15        18.18        19.33         9.93        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        9.70        30.28        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       13.55        19.10        37.74        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-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-3605 
       36.03        20.05         1.02        46.03        34.03         0.99 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       19.99        19.99         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03         0.99         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
       36.03         9.07        12.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97         1.94        38.96        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        0.72        26.43         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        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.99        12.00        15.02        36.00        10.98        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       16.41        11.51        10.78        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        55.76        47.08        26.43 

$`AMP PEAK 16(13Q22.1) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       42.90        24.33        37.05        37.25        37.02        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.00        19.07        33.99        17.95        29.95        23.01 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       61.02         6.97         0.92        47.05        47.01        11.01 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 
       36.00         5.03        26.99        19.04        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 
       17.98        15.95        38.99         0.00         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00        36.03        31.07        53.00        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        24.00        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        18.05         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       34.98        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02        39.06        51.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
       22.03        18.05        56.55        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       27.09         0.20        17.82        17.85        19.33        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
        5.65        32.94        83.80        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        45.40        20.19        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A1D8 
       15.58        12.39         9.44        11.64         1.51        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G 
      140.38        44.32       135.65       139.17        81.37        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 
       13.45        35.87         1.55        16.31        19.43        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        55.04        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GC 
       13.78        26.17        52.80        10.98        19.33        12.79 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 
       31.30        70.03        12.72        16.83        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       32.02         8.02        24.00         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        6.05        15.95         7.99         1.02        32.98         0.99 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J 
       13.02        48.03        20.98        13.94        37.02         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       31.00        10.98        61.97        41.00         1.45         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 
       10.19         6.05        13.97        12.95         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 
       20.91         8.61        13.64        17.46         8.45         0.53 
TCGA-F5-6861 TCGA-F5-6864 
        1.12         0.46 

  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE 
                         19.00                          19.38 
[1] "0.1 - 131.5 (19.0)" "0.0 - 140.4 (19.4)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   273 117
  AMP PEAK 16(13Q22.1) WILD-TYPE 169  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    273  117
  AMP PEAK 16(13Q22.1) WILD-TYPE  169   45
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON                           273                            169
  RECTUM                          117                             45
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(13Q22.1) MUTATED        65        0       20        93         4
  AMP PEAK 16(13Q22.1) WILD-TYPE      39        1       16        78         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(13Q22.1) MUTATED           3        16         17         58
  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           40       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                              65                             39
  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                           58                             21
  STAGE IIIC                           40                             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  66 268  44
  AMP PEAK 16(13Q22.1) WILD-TYPE   5  41 145  22
D16V5, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  T1                           15                              5
  T2                           66                             41
  T3                          268                            145
  T4                           44                             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   195 112  84
  AMP PEAK 16(13Q22.1) WILD-TYPE 147  37  30
D16V6, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  N0                          195                            147
  N1                          112                             37
  N2                           84                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   278  66
  AMP PEAK 16(13Q22.1) WILD-TYPE 170  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    278   66
  AMP PEAK 16(13Q22.1) WILD-TYPE  170   20
   clus
vv  AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  0                          278                            170
  1                           66                             20
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(13Q22.1) MUTATED   177 217
  AMP PEAK 16(13Q22.1) WILD-TYPE 109 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED    177  217
  AMP PEAK 16(13Q22.1) WILD-TYPE  109  105
        clus
vv       AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  FEMALE                          177                            109
  MALE                            217                            105
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                    253
  AMP PEAK 16(13Q22.1) WILD-TYPE                  128
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(13Q22.1) MUTATED                              20
  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                                    253
  COLON MUCINOUS ADENOCARCINOMA                            20
  RECTAL ADENOCARCINOMA                                   112
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 16(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  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     7 387
  AMP PEAK 16(13Q22.1) WILD-TYPE   2 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(13Q22.1) MUTATED      7  387
  AMP PEAK 16(13Q22.1) WILD-TYPE    2  212
     clus
vv    AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  NO                             7                              2
  YES                          387                            212
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(13Q22.1) MUTATED   278   3  26  14
  AMP PEAK 16(13Q22.1) WILD-TYPE 161   2  10  15
D16V11, multiclass
    clus
vv   AMP PEAK 16(13Q22.1) MUTATED AMP PEAK 16(13Q22.1) WILD-TYPE
  R0                          278                            161
  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                          40   201
  AMP PEAK 16(13Q22.1) WILD-TYPE                        20    91
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  40
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 16(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  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(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 438 105
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            40                            543 
  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                            10                            105 
$`AMP PEAK 17(15Q26.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-6649 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3560 
       11.47        43.76        24.16        29.00        29.00        19.99 
TCGA-AA-3681 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 TCGA-AA-A02H TCGA-AY-4070 
        5.98        36.03         0.99        24.00         2.01        16.31 
TCGA-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        42.77        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         7.17 
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-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        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 
       16.57        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
       10.06         0.00        33.07         0.00        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-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-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84        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        49.08        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        25.02        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        45.40        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        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.80        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        13.25 
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        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       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        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        13.05        12.00 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30         9.70        30.28 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95         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-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-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        0.49         1.45         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
        6.05         6.97         4.73        13.97        78.12        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        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        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-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97        37.51        31.30        28.57         0.39        32.19 
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 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE 
                           0.2                            0.0 
  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                          19.07 
[1] "0.2 - 82.4 (18.9)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    29  13
  AMP PEAK 17(15Q26.1) WILD-TYPE 413 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     29   13
  AMP PEAK 17(15Q26.1) WILD-TYPE  413  149
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  COLON                            29                            413
  RECTUM                           13                            149
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(15Q26.1) MUTATED         5        0        1        11         0
  AMP PEAK 17(15Q26.1) WILD-TYPE      99        1       35       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         74
                                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         43       56        24         2
D17V4, multiclass
            clus
vv           AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            11                            160
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             1                             25
  STAGE IIIA                            0                             21
  STAGE IIIB                            5                             74
  STAGE IIIC                           11                             43
  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  19 103 383  59
D17V5, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  T1                            1                             19
  T2                            4                            103
  T3                           30                            383
  T4                            7                             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 17(15Q26.1) MUTATED    17   8  17
  AMP PEAK 17(15Q26.1) WILD-TYPE 325 141  97
D17V6, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  N0                           17                            325
  N1                            8                            141
  N2                           17                             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"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    31   7
  AMP PEAK 17(15Q26.1) WILD-TYPE 417  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     31    7
  AMP PEAK 17(15Q26.1) WILD-TYPE  417   79
   clus
vv  AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  0                           31                            417
  1                            7                             79
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED    24  18
  AMP PEAK 17(15Q26.1) WILD-TYPE 262 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED     24   18
  AMP PEAK 17(15Q26.1) WILD-TYPE  262  304
        clus
vv       AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  FEMALE                           24                            262
  MALE                             18                            304
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                     25
  AMP PEAK 17(15Q26.1) WILD-TYPE                  356
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                               4
  AMP PEAK 17(15Q26.1) WILD-TYPE                            56
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                      11
  AMP PEAK 17(15Q26.1) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(15Q26.1) MUTATED                                2
  AMP PEAK 17(15Q26.1) WILD-TYPE                             11
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                                      356
  COLON MUCINOUS ADENOCARCINOMA                              56
  RECTAL ADENOCARCINOMA                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(15Q26.1) MUTATED     2  40
  AMP PEAK 17(15Q26.1) WILD-TYPE   7 559
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(15Q26.1) MUTATED      2   40
  AMP PEAK 17(15Q26.1) WILD-TYPE    7  559
     clus
vv    AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  NO                             2                              7
  YES                           40                            559
[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 409   4  33  27
D17V11, multiclass
    clus
vv   AMP PEAK 17(15Q26.1) MUTATED AMP PEAK 17(15Q26.1) WILD-TYPE
  R0                           30                            409
  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                        57   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                                    57
  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  29
  AMP PEAK 18(16P11.2) WILD-TYPE 337  86
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                           160                            423 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            29                             86 
$`AMP PEAK 18(16P11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.76        43.43        24.33        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       16.57        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-3852 TCGA-AA-3856 TCGA-AA-3860 
       14.93        17.03        33.07         0.00         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 
       17.03        24.03        27.02        29.98         2.01        12.99 
TCGA-AA-3941 TCGA-AA-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-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T 
       27.02        34.03        42.02        15.02        12.00        33.04 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 
       41.00        40.96        22.42        27.42         0.20         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
       15.75         0.20        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 
       29.56         5.23         1.94         2.24         3.29         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
      102.44        49.08        21.99        20.02         8.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       22.03        22.98        16.01        17.03        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 
       21.99        14.99        15.02        11.01        10.06        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 
       18.25         1.32        15.12        17.13        12.49        10.13 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 
       13.41        11.38        38.20        13.32        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       13.38         1.55        82.39        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 
       55.04        45.11        39.42        35.93        26.43        13.78 
TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3911 
       46.75        15.65        12.79         9.70        39.48        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 
       10.39        15.39        20.02        86.63        65.98        36.03 
TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 
        6.05         7.99         1.02        17.03        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         0.99        15.95        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 
       31.00        38.96        38.04         0.72        10.19         6.97 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 
        9.37        78.12        11.01        12.99        12.00        10.06 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       24.13        51.48         0.49        17.69        16.31        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       28.57         0.39        32.19         0.76 

$`AMP PEAK 18(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       42.28        13.94        37.05        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       14.53        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        22.52         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        10.06         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 
        0.00        36.03        32.05        31.07        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3968 
       31.00        33.01        26.01        24.00         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       50.99        13.05        34.06        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-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-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         5.79        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09        16.31        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65        32.94        83.80        22.36        65.00        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.14         2.93         2.01       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 
       25.02        26.04        27.02        29.06        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        20.42        17.75        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.80        16.14        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
      119.93        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21         8.35        23.51        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       26.17        91.79        47.15        52.80        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        13.05        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       29.46        32.98         8.42        31.30        30.28        70.03 
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        16.83        10.39        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-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        26.43         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         7.17        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        10.98        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                              0 
  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 
                         19.99                          19.04 
[1] "0.0 - 102.4 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   122  47
  AMP PEAK 18(16P11.2) WILD-TYPE 320 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    122   47
  AMP PEAK 18(16P11.2) WILD-TYPE  320  115
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  COLON                           122                            320
  RECTUM                           47                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(16P11.2) MUTATED        20        1        4        37         3
  AMP PEAK 18(16P11.2) WILD-TYPE      84        0       32       134         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(16P11.2) MUTATED           0         6         10         31
  AMP PEAK 18(16P11.2) WILD-TYPE         3        20         11         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(16P11.2) MUTATED           21       23         8         1
  AMP PEAK 18(16P11.2) WILD-TYPE         33       38        19         1
D18V4, multiclass
            clus
vv           AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              1                              0
  STAGE II                              4                             32
  STAGE IIA                            37                            134
  STAGE IIB                             3                              7
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                           10                             11
  STAGE IIIB                           31                             48
  STAGE IIIC                           21                             33
  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  26 121  17
  AMP PEAK 18(16P11.2) WILD-TYPE  15  81 292  49
D18V5, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  T1                            5                             15
  T2                           26                             81
  T3                          121                            292
  T4                           17                             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 18(16P11.2) MUTATED    71  55  43
  AMP PEAK 18(16P11.2) WILD-TYPE 271  94  71
D18V6, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  N0                           71                            271
  N1                           55                             94
  N2                           43                             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"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED   114  32
  AMP PEAK 18(16P11.2) WILD-TYPE 334  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED    114   32
  AMP PEAK 18(16P11.2) WILD-TYPE  334   54
   clus
vv  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  0                          114                            334
  1                           32                             54
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(16P11.2) MUTATED    81  89
  AMP PEAK 18(16P11.2) WILD-TYPE 205 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED     81   89
  AMP PEAK 18(16P11.2) WILD-TYPE  205  233
        clus
vv       AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  FEMALE                           81                            205
  MALE                             89                            233
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                    114
  AMP PEAK 18(16P11.2) WILD-TYPE                  267
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(16P11.2) MUTATED                               8
  AMP PEAK 18(16P11.2) WILD-TYPE                            52
                                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                                    114
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 18(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      267
  COLON MUCINOUS ADENOCARCINOMA                              52
  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     4 166
  AMP PEAK 18(16P11.2) WILD-TYPE   5 433
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(16P11.2) MUTATED      4  166
  AMP PEAK 18(16P11.2) WILD-TYPE    5  433
     clus
vv    AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  NO                             4                              5
  YES                          166                            433
[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 316   5  22  22
D18V11, multiclass
    clus
vv   AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE
  R0                          123                            316
  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                          17    83
  AMP PEAK 18(16P11.2) WILD-TYPE                        43   209
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK 18(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    43
  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   130  20
  AMP PEAK 19(17Q12) WILD-TYPE 338  95
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                         150                          433 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          20                           95 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 
       11.47        11.47        43.76        43.43        24.33        37.02 
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-3529 
       37.05         1.02        58.03        38.99        36.03         0.00 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 
       29.00        12.99        24.00        23.01        15.02        36.00 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 
       85.05        35.05         1.02        17.03         0.99        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 
       27.02        18.05        12.99        34.03         2.01        50.99 
TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01F 
       13.05        27.02        27.02        38.04        21.99        32.02 
TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 
       12.00         1.02         0.92        41.00         4.21         0.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6600 
       27.42        16.44        16.31        18.84        61.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 
       29.56         3.19         2.24         0.07         1.35       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-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       19.59        11.51        18.25         1.32        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       17.13        14.30        13.41        24.43        38.20       130.65 
TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 
        6.12        95.18         1.55        74.56        65.85        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-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2690 
       15.65        13.05        29.46        32.98        30.28        17.23 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       86.63        65.98        11.84        12.00         7.07        36.03 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3742 
       46.03        34.03        15.95        19.99        19.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       19.99         1.02        48.03        32.02        36.03         1.02 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 
       17.03        15.95         9.07        31.00        64.01        51.98 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 
        0.69        26.43         6.05         9.37        12.00        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 
       10.06         5.29        51.48        17.00        18.28        16.31 
TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
       11.97        32.19         0.69         0.46        55.76        26.43 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
        4.80        43.76        46.65        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       22.09        22.06        22.52        24.13         8.38        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        7.04         3.02        35.01        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       13.02         1.02         9.07        24.03        37.05         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-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        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        19.04        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
        0.99        25.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        29.98        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        25.02        24.00        19.07         7.96 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01I 
       14.99        34.98        15.02        15.02        10.98        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37        56.55         0.72         5.79        22.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-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        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        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-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         3.06         2.14         3.25         3.29         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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       49.08        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        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.98        30.08        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-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       10.06        12.03        45.40        12.26        13.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       20.42        17.75        43.27        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
       28.21         8.35        82.39        23.51        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       44.68        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        47.15        52.80        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        12.79        12.00 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       42.77         8.42        31.30         9.70        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        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        16.83        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        20.05        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        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        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        10.98        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        28.57 
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                            0 
  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 
                       19.99                        19.04 
[1] "0.0 - 130.7 (20.0)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.6"
D19V2, continuous
D19V3, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   112  46
  AMP PEAK 19(17Q12) WILD-TYPE 330 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    112   46
  AMP PEAK 19(17Q12) WILD-TYPE  330  116
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  COLON                         112                          330
  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      82        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         59
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(17Q12) MUTATED           19       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                           82
  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                           59
  STAGE IIIC                         19                           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  22 112  16
  AMP PEAK 19(17Q12) WILD-TYPE  12  85 301  50
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  T1                          8                           12
  T2                         22                           85
  T3                        112                          301
  T4                         16                           50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 19(17Q12) MUTATED    81  38  38
  AMP PEAK 19(17Q12) WILD-TYPE 261 111  76
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  N0                         81                          261
  N1                         38                          111
  N2                         38                           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"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED   102  33
  AMP PEAK 19(17Q12) WILD-TYPE 346  53
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED    102   33
  AMP PEAK 19(17Q12) WILD-TYPE  346   53
   clus
vv  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  0                        102                          346
  1                         33                           53
[1] 2 2
[1] FALSE
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(17Q12) MUTATED    66  92
  AMP PEAK 19(17Q12) WILD-TYPE 220 230
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED     66   92
  AMP PEAK 19(17Q12) WILD-TYPE  220  230
        clus
vv       AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  FEMALE                         66                          220
  MALE                           92                          230
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                     99
  AMP PEAK 19(17Q12) WILD-TYPE                  282
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q12) MUTATED                              12
  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                          12
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 19(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    282
  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     1 157
  AMP PEAK 19(17Q12) WILD-TYPE   8 442
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(17Q12) MUTATED      1  157
  AMP PEAK 19(17Q12) WILD-TYPE    8  442
     clus
vv    AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  NO                           1                            8
  YES                        157                          442
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 19(17Q12) MUTATED   108   2  16   6
  AMP PEAK 19(17Q12) WILD-TYPE 331   3  20  23
D19V11, multiclass
    clus
vv   AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE
  R0                        108                          331
  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                          19    71
  AMP PEAK 19(17Q12) WILD-TYPE                        41   221
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                19
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 19(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  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(20) Variable = AMP PEAK 20(17Q24.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(17Q24.1) MUTATED   122  15
  AMP PEAK 20(17Q24.1) WILD-TYPE 346 100
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                           137                            446 
  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE 
                            15                            100 
$`AMP PEAK 20(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
       11.47         4.80        11.47        43.43        24.33        42.28 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 
       37.02        36.53        14.53        30.44        29.19        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 
       29.16        27.09        25.08        25.18        24.69        20.28 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 
        1.02        37.05         1.02        58.03        24.00        23.01 
TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 
       15.02        36.00        85.05        35.05         1.02        17.03 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 
       10.06        36.03         0.99        24.03        12.99        24.00 
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-3982 TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S 
       27.02        13.94        38.04        21.99        12.00         1.02 
TCGA-AA-A01Z TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
       37.02        41.00         4.21         0.79        27.42        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-6715 
       14.50        16.31        61.41        29.56         2.24         0.07 
TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 
      102.44         8.02        13.02        29.06        22.03        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        21.99        14.99        13.05        11.08 
TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 
       11.01        12.26        19.59        11.51         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 
        4.80        17.13        14.30        13.41       130.65         6.12 
TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       95.18        74.56        65.85        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GB 
       35.93        36.00        26.43        91.79        46.75        15.65 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 
       13.05        29.46        32.98        30.28        39.48        17.23 
TCGA-AF-2692 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 
       13.55        86.63        11.84        12.00         7.07        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 
       34.03        50.04        15.95        19.99        19.99        19.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N 
       36.03         1.02        17.03        15.95         9.07        31.00 
TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 
       51.98         0.69        26.43         6.05        12.00        13.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 
       10.06       129.27        51.48         0.49         2.40        18.28 
TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6235 
       16.31        11.97        32.19         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 
       43.76        46.65        43.76        42.90        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        37.25        34.65 
TCGA-A6-4107 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        56.25         9.63         5.03         7.04 
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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       21.01        13.02        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       47.01        11.01         5.98        37.05        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        19.04        10.06         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
        0.00         0.00        33.07         0.00        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
       31.00         2.01        24.00        33.01        26.01         2.01 
TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       20.98        16.08        26.01        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-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-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       33.04        35.01        26.01        39.06        51.98         2.96 
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-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 
        5.79        22.42        10.88         0.20         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-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.26        17.85        19.33        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56        40.34        70.16        15.62        49.08 
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        25.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       15.02        14.04        11.01        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        45.40        13.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       67.30        53.62        44.68        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       12.00        42.77         8.42        31.30         9.70        70.03 
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        16.83        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        36.03        20.05        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        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        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        10.98        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        28.57         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                           0.00 
  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 
                         20.28                          19.00 
[1] "0.1 - 130.7 (20.3)" "0.0 - 140.4 (19.0)"
[1] "hr=" "2.2"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED   103  38
  AMP PEAK 20(17Q24.1) WILD-TYPE 339 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED    103   38
  AMP PEAK 20(17Q24.1) WILD-TYPE  339  124
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON                           103                            339
  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      83        1       32       130         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(17Q24.1) MUTATED           1         5          4         21
  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           13       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                             83
  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                           21                             58
  STAGE IIIC                           13                             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  24 101  13
  AMP PEAK 20(17Q24.1) WILD-TYPE  16  83 312  53
D20V5, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  T1                            4                             16
  T2                           24                             83
  T3                          101                            312
  T4                           13                             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  36  27
  AMP PEAK 20(17Q24.1) WILD-TYPE 264 113  87
D20V6, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  N0                           78                            264
  N1                           36                            113
  N2                           27                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED    95  26
  AMP PEAK 20(17Q24.1) WILD-TYPE 353  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED     95   26
  AMP PEAK 20(17Q24.1) WILD-TYPE  353   60
   clus
vv  AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  0                           95                            353
  1                           26                             60
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(17Q24.1) MUTATED    70  72
  AMP PEAK 20(17Q24.1) WILD-TYPE 216 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED     70   72
  AMP PEAK 20(17Q24.1) WILD-TYPE  216  250
        clus
vv       AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  FEMALE                           70                            216
  MALE                             72                            250
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                     92
  AMP PEAK 20(17Q24.1) WILD-TYPE                  289
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                              10
  AMP PEAK 20(17Q24.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                      38
  AMP PEAK 20(17Q24.1) WILD-TYPE                   108
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(17Q24.1) MUTATED                                0
  AMP PEAK 20(17Q24.1) WILD-TYPE                             13
D20V9, multiclass
                                clus
vv                               AMP PEAK 20(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                     92
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      289
  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     1 141
  AMP PEAK 20(17Q24.1) WILD-TYPE   8 458
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(17Q24.1) MUTATED      1  141
  AMP PEAK 20(17Q24.1) WILD-TYPE    8  458
     clus
vv    AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  NO                             1                              8
  YES                          141                            458
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(17Q24.1) MUTATED   103   2  12   3
  AMP PEAK 20(17Q24.1) WILD-TYPE 336   3  24  26
D20V11, multiclass
    clus
vv   AMP PEAK 20(17Q24.1) MUTATED AMP PEAK 20(17Q24.1) WILD-TYPE
  R0                          103                            336
  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                          17    71
  AMP PEAK 20(17Q24.1) WILD-TYPE                        43   221
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      71
                                  clus
vv                                 AMP PEAK 20(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       221
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(19P13.2) MUTATED    82  20
  AMP PEAK 21(19P13.2) WILD-TYPE 386  95
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                           102                            481 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            20                             95 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 
       11.47        11.47        43.76        43.43        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       16.57        36.53        14.53        31.63        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 
       21.76        23.87        56.25         9.07         6.05         2.01 
TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 
       37.05        35.05         0.99        31.07        50.99        13.05 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O 
       27.02        13.94        42.02        32.02        51.98         0.92 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-A8YK 
        5.79        22.42        16.44         0.46        16.31        18.84 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       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        25.02        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-QG-A5YW TCGA-QL-A97D TCGA-AF-2690 
       26.43        47.15        13.05        29.46         9.70        17.23 
TCGA-AF-3913 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 
       10.39        86.63        65.98        36.03         6.05        19.99 
TCGA-AG-3878 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
        0.99         1.02        28.04        36.03         1.02         0.99 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 
       12.00        31.00         1.94        38.04        10.98        11.01 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
       12.00        36.00        13.05        57.24        24.13         0.49 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6863 
       20.55        17.69        16.31        11.51        11.97         0.76 

$`AMP PEAK 21(19P13.2) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        4.80        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        13.94        37.05        37.25        37.02        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-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        19.04        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-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-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07         7.96        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-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-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        27.42        10.88 
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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
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 
       49.08        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 
       45.40        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        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 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        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       65.85        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        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        12.00        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        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        16.83        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        20.05 
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        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        15.02        10.98 
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        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         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 
                          0.46                           0.00 
  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 
                        18.265                         19.070 
[1] "0.5 - 86.6 (18.3)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    75  36
  AMP PEAK 21(19P13.2) WILD-TYPE 367 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     75   36
  AMP PEAK 21(19P13.2) WILD-TYPE  367  126
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  COLON                            75                            367
  RECTUM                           36                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(19P13.2) MUTATED        14        0        6        28         2
  AMP PEAK 21(19P13.2) WILD-TYPE      90        1       30       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         59
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(19P13.2) MUTATED           11       12         6         0
  AMP PEAK 21(19P13.2) WILD-TYPE         43       49        21         2
D21V4, multiclass
            clus
vv           AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  STAGE I                              14                             90
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            28                            143
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            3                             18
  STAGE IIIB                           20                             59
  STAGE IIIC                           11                             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  15  81  13
  AMP PEAK 21(19P13.2) WILD-TYPE  18  92 332  53
D21V5, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  T1                            2                             18
  T2                           15                             92
  T3                           81                            332
  T4                           13                             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 21(19P13.2) MUTATED    55  36  20
  AMP PEAK 21(19P13.2) WILD-TYPE 287 113  94
D21V6, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  N0                           55                            287
  N1                           36                            113
  N2                           20                             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"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    74  18
  AMP PEAK 21(19P13.2) WILD-TYPE 374  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     74   18
  AMP PEAK 21(19P13.2) WILD-TYPE  374   68
   clus
vv  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  0                           74                            374
  1                           18                             68
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(19P13.2) MUTATED    47  64
  AMP PEAK 21(19P13.2) WILD-TYPE 239 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED     47   64
  AMP PEAK 21(19P13.2) WILD-TYPE  239  258
        clus
vv       AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  FEMALE                           47                            239
  MALE                             64                            258
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                     67
  AMP PEAK 21(19P13.2) WILD-TYPE                  314
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                               8
  AMP PEAK 21(19P13.2) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                      36
  AMP PEAK 21(19P13.2) WILD-TYPE                   110
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19P13.2) MUTATED                                0
  AMP PEAK 21(19P13.2) WILD-TYPE                             13
D21V9, multiclass
                                clus
vv                               AMP PEAK 21(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                     67
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 21(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      314
  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     1 110
  AMP PEAK 21(19P13.2) WILD-TYPE   8 489
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(19P13.2) MUTATED      1  110
  AMP PEAK 21(19P13.2) WILD-TYPE    8  489
     clus
vv    AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  NO                             1                              8
  YES                          110                            489
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(19P13.2) MUTATED    80   3   6   7
  AMP PEAK 21(19P13.2) WILD-TYPE 359   2  30  22
D21V11, multiclass
    clus
vv   AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE
  R0                           80                            359
  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                          17    57
  AMP PEAK 21(19P13.2) WILD-TYPE                        43   235
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 21(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    43
  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   105  22
  AMP PEAK 22(19Q12) WILD-TYPE 363  93
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                         127                          456 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          22                           93 
$`AMP PEAK 22(19Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
       11.47        11.47        43.76        43.43        45.60        16.57 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 
       37.02        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        56.25 
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         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D 
       22.42         0.20        16.44        14.50         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 
       18.84        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        25.02        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         4.80        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-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3913 
       47.15        13.05        29.46         9.70        39.48        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 
       86.63        65.98        36.03        46.03         6.05        19.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 
        0.99        19.99         1.02        36.03         1.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 
       36.03         9.07        12.00        31.00         1.94        38.04 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
       10.19         6.05         4.73        13.97        10.98        11.01 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
       12.00        36.00        13.05       129.27        24.13         0.49 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
       20.55        17.69        16.31        11.51        13.64        11.97 
TCGA-F5-6863 
        0.76 

$`AMP PEAK 22(19Q12) WILD-TYPE`
TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        4.80        46.65        43.76        42.90        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 
       44.91        35.11        13.94        37.05        37.25        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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05         1.02        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        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-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-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-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       19.04        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00         0.00        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        38.04         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02H 
       33.04        35.01        26.01        37.02        39.06         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37        56.55         0.79         0.72        27.42 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       15.75        21.44        17.82        17.26        19.33        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        49.08 
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 
       45.40        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        43.27        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        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       65.85        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        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        12.00 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       42.77        32.98         8.42        31.30        30.28        70.03 
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        16.83        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 
       20.05        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 
       26.43         1.81         6.05         6.97         9.37        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.17        15.02        12.99        13.97        15.02        10.98 
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 
       28.57         0.39        32.19         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 
                         0.2                          0.0 
  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 
                      18.050                       19.085 
[1] "0.2 - 129.3 (18.1)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D22V2, continuous
D22V3, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    94  44
  AMP PEAK 22(19Q12) WILD-TYPE 348 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     94   44
  AMP PEAK 22(19Q12) WILD-TYPE  348  118
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  COLON                          94                          348
  RECTUM                         44                          118
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(19Q12) MUTATED        22        0        5        35         1
  AMP PEAK 22(19Q12) WILD-TYPE      82        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         58
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(19Q12) MUTATED           13       22         6         0
  AMP PEAK 22(19Q12) WILD-TYPE         41       39        21         2
D22V4, multiclass
            clus
vv           AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  STAGE I                            22                           82
  STAGE IA                            0                            1
  STAGE II                            5                           31
  STAGE IIA                          35                          136
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          4                           17
  STAGE IIIB                         21                           58
  STAGE IIIC                         13                           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  23  96  16
  AMP PEAK 22(19Q12) WILD-TYPE  17  84 317  50
D22V5, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  T1                          3                           17
  T2                         23                           84
  T3                         96                          317
  T4                         16                           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 22(19Q12) MUTATED    68  42  27
  AMP PEAK 22(19Q12) WILD-TYPE 274 107  87
D22V6, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  N0                         68                          274
  N1                         42                          107
  N2                         27                           87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    89  28
  AMP PEAK 22(19Q12) WILD-TYPE 359  58
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     89   28
  AMP PEAK 22(19Q12) WILD-TYPE  359   58
   clus
vv  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  0                         89                          359
  1                         28                           58
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED    59  79
  AMP PEAK 22(19Q12) WILD-TYPE 227 243
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED     59   79
  AMP PEAK 22(19Q12) WILD-TYPE  227  243
        clus
vv       AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  FEMALE                         59                          227
  MALE                           79                          243
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                     84
  AMP PEAK 22(19Q12) WILD-TYPE                  297
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                              10
  AMP PEAK 22(19Q12) WILD-TYPE                            50
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                      44
  AMP PEAK 22(19Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(19Q12) MUTATED                                0
  AMP PEAK 22(19Q12) WILD-TYPE                             13
D22V9, multiclass
                                clus
vv                               AMP PEAK 22(19Q12) MUTATED
  COLON ADENOCARCINOMA                                   84
  COLON MUCINOUS ADENOCARCINOMA                          10
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          0
                                clus
vv                               AMP PEAK 22(19Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    297
  COLON MUCINOUS ADENOCARCINOMA                            50
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                           13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                              cls
clus                             0   1
  AMP PEAK 22(19Q12) MUTATED     2 136
  AMP PEAK 22(19Q12) WILD-TYPE   7 463
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(19Q12) MUTATED      2  136
  AMP PEAK 22(19Q12) WILD-TYPE    7  463
     clus
vv    AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  NO                           2                            7
  YES                        136                          463
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(19Q12) MUTATED    97   2  11   7
  AMP PEAK 22(19Q12) WILD-TYPE 342   3  25  22
D22V11, multiclass
    clus
vv   AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE
  R0                         97                          342
  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                          18    70
  AMP PEAK 22(19Q12) WILD-TYPE                        42   222
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                    70
                                  clus
vv                                 AMP PEAK 22(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                  42
  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   211  53
  AMP PEAK 23(20P12.1) WILD-TYPE 257  62
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                           264                            319 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                            53                             62 
$`AMP PEAK 23(20P12.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
       11.47         4.80        43.76        43.76        43.43        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        16.57        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6137 TCGA-A6-6142 
       36.53        32.45        32.91        30.44        27.09        25.08 
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-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 
        7.04         1.02        58.03         6.97         1.02        24.03 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 
        0.00        19.07        29.00        29.00        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 
       13.02        23.01        20.98        19.99         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.05        15.02        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 
       36.00         5.03        10.06         0.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
        0.00        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3968 
       17.03        18.05        12.99        24.00        34.03        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-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.07         7.96        13.94        18.05        38.04         4.01 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       31.00        33.04        26.01        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 
        5.03         0.92        41.00        39.98         0.07         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 
        0.72         5.79        22.42        27.42        16.44        16.31 
TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 
        0.95        17.26        17.85        19.33        18.84         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        83.80        65.00        49.41        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19         2.24         3.06         2.14         3.29         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-4744 TCGA-CM-4747 
        1.35        17.56        40.34        49.08        20.02        25.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       13.02        29.06        22.98         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6171 
       17.03        15.02        14.04        16.04        21.99        14.04 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        11.08        11.01        45.40        12.26        19.59 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
       20.19        17.75        12.49        12.39        10.13         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D8 TCGA-DM-A1DA 
       11.64        13.41        10.26       119.70        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
       44.32       139.17         6.12        14.04        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 
       95.18         8.61        13.45         6.18         1.55        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
      107.67        28.21        82.39        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.00        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
       47.15        18.18        15.65        12.79        13.05        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 
       29.46        32.98        24.13        17.23        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3580 
       10.39        14.50        16.83        20.02        10.39         8.02 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       36.03         1.02        46.03        50.04        12.03         0.99 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3887 
       19.99        19.99        29.98         1.02         0.99        36.95 
TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       17.03        14.01        48.03        19.99        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       17.03         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        9.07        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        26.43         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        9.37        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DE 
       13.97        15.02        36.00        12.95       126.44       129.27 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6885 
       20.55        20.91        17.00        18.28        16.31        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97         9.96        37.51         0.39        32.19         0.66 
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 

$`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 
       11.47        46.65        42.90        24.33        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        56.25         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        19.04        35.05        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3850 
        1.02        17.98        15.95        38.99        36.95         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 
        0.00        36.03        32.05        31.07        53.00        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3977 
       24.00         2.01        20.98         2.01        16.08        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       27.02        42.02         0.99        34.98        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J 
       37.02        39.06        39.98        22.03        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       21.37         4.21        56.55        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        14.50        27.09        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.82        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       22.36        62.79        61.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       11.74         1.94         3.25         0.26         0.33         0.10 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        70.16        15.62        51.32        21.99        21.14 
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-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        27.02        22.03        30.08        16.01        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       12.00        29.03        14.99        12.99        13.02        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 
       12.95        13.05        11.08        10.06        12.03        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.42        18.25         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
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-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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C 
      140.38       131.51       135.65         7.76        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      119.93        60.79        98.24        13.38        11.11        13.64 
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        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43         8.35        23.51        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 
       65.85        53.62        44.68        51.75        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       22.09        35.80        26.17        52.80        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       19.33         9.93        12.00         8.42        31.30         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       30.28        70.03        39.48        43.04        13.55        12.72 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 
       32.02         7.07        20.05        24.00        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
        6.05        15.95         7.99         0.99        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 
       19.99         1.02        13.02        35.01         1.02        32.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A014 
       28.04        36.03         0.99        20.98        13.94        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-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 
       49.97         1.94        38.96        61.97         1.45         6.05 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
        4.73        78.12         7.17        12.00        10.98        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06         5.29        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 
       51.48        32.61         0.49         2.40        19.96        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       17.46         8.45        31.30        28.57         0.69         0.46 
TCGA-G5-6641 
       26.43 

  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                             0                              0 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                        139.17                         140.38 
  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE 
                         17.13                          20.98 
[1] "0.0 - 139.2 (17.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   193  81
  AMP PEAK 23(20P12.1) WILD-TYPE 249  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    193   81
  AMP PEAK 23(20P12.1) WILD-TYPE  249   81
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  COLON                           193                            249
  RECTUM                           81                             81
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20P12.1) MUTATED        50        1       10        68         4
  AMP PEAK 23(20P12.1) WILD-TYPE      54        0       26       103         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20P12.1) MUTATED           1        10         13         30
  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           24       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                              50                             54
  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                           30                             49
  STAGE IIIC                           24                             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  52 184  30
  AMP PEAK 23(20P12.1) WILD-TYPE  11  55 229  36
D23V5, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  T1                            9                             11
  T2                           52                             55
  T3                          184                            229
  T4                           30                             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  75  58
  AMP PEAK 23(20P12.1) WILD-TYPE 200  74  56
D23V6, multiclass
    clus
vv   AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  N0                          142                            200
  N1                           75                             74
  N2                           58                             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"
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   185  54
  AMP PEAK 23(20P12.1) WILD-TYPE 263  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    185   54
  AMP PEAK 23(20P12.1) WILD-TYPE  263   32
   clus
vv  AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  0                          185                            263
  1                           54                             32
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED   117 160
  AMP PEAK 23(20P12.1) WILD-TYPE 169 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED    117  160
  AMP PEAK 23(20P12.1) WILD-TYPE  169  162
        clus
vv       AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  FEMALE                          117                            169
  MALE                            160                            162
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                    174
  AMP PEAK 23(20P12.1) WILD-TYPE                  207
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                              18
  AMP PEAK 23(20P12.1) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                      76
  AMP PEAK 23(20P12.1) WILD-TYPE                    70
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P12.1) MUTATED                                3
  AMP PEAK 23(20P12.1) WILD-TYPE                             10
D23V9, multiclass
                                clus
vv                               AMP PEAK 23(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    174
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                    76
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK 23(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      207
  COLON MUCINOUS ADENOCARCINOMA                              42
  RECTAL ADENOCARCINOMA                                      70
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                                cls
clus                               0   1
  AMP PEAK 23(20P12.1) MUTATED     7 270
  AMP PEAK 23(20P12.1) WILD-TYPE   2 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(20P12.1) MUTATED      7  270
  AMP PEAK 23(20P12.1) WILD-TYPE    2  329
     clus
vv    AMP PEAK 23(20P12.1) MUTATED AMP PEAK 23(20P12.1) WILD-TYPE
  NO                             7                              2
  YES                          270                            329
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(20P12.1) MUTATED   197   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                          197                            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                          26   132
  AMP PEAK 23(20P12.1) WILD-TYPE                        34   160
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK 23(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    34
  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   277  67
  AMP PEAK 24(20P11.21) WILD-TYPE 191  48
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                            344                             239 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                             67                              48 
$`AMP PEAK 24(20P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 
       44.91        35.11        45.60        13.94        16.57        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 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-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       29.19        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU 
       25.18        24.16        24.69        20.28        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         7.04         1.02         1.02        58.03         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
        1.02        38.99         0.00        19.07        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 
       12.99        14.01        21.01        13.02        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       19.99        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-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-3697 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 
       85.05        10.06         0.99        25.02        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       14.93         0.00        17.03        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       31.07        17.03        27.02        18.05        12.99        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-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U 
        7.96        13.94        18.05        38.04         4.01        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        21.99        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       31.00        33.04        26.01        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        0.07        21.37         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42         0.20        16.44        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 
        0.20        17.26        17.85        19.33        18.84         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        83.80        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        3.29         0.07         0.26         1.35        17.56        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       49.08        21.99        20.02        25.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 
       21.99        13.02        15.02        14.04        11.01        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.01        10.06        45.40        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 
       20.19        17.75        18.25         1.32        43.27        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
        7.53        12.39        10.13         9.04        11.64        13.41 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA 
       10.26       119.70        24.43       130.65        12.59         7.50 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F 
      131.51       139.17         6.12        14.04       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        95.18         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 
        1.55        33.67        13.25        35.41       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        8.35        82.39        23.51        65.85        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        35.93        36.72        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC 
       91.79        46.75        47.15        18.18        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       13.05        42.77        29.46        32.98         8.42         9.70 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        39.48        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 
       16.83        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        36.03        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        26.43         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        78.12         7.17        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        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         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 
       11.47        46.65        42.90        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        56.25         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        19.04        35.05 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95        36.95         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 
       36.03        32.05        31.07        53.00        24.03        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       25.02        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01F 
       18.05        27.02        42.02         0.99        34.98        32.02 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6888 TCGA-AD-6889 
       37.02        39.06        22.03        18.05         4.21        56.55 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
       10.88         0.46         0.92        27.09        15.75        21.44 
TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.82        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36        61.41         6.77       100.01         5.23        11.74 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        3.25         0.33         0.10       102.44        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-4748 TCGA-CM-4751 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 
       37.02        26.04        27.02        30.08        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       14.99        12.99        12.95        13.05        11.08        12.03 
TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       13.51        20.42        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       16.14        15.58        12.43        14.30         9.44         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00        11.38        38.20        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C 
      140.38        44.32       135.65         7.76        26.47        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 
       60.79        98.24        11.11        13.64        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 
       29.59        16.24         0.53        19.43        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 
       53.62        51.75        36.00        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        19.33        19.33         9.93 
TCGA-NH-A8F8 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       12.00        31.30        30.28        70.03        43.04        13.55 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 
       12.72        14.50        15.39        65.98        12.00        32.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 
       20.05        24.00         1.02         2.01         6.05         0.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4022 
        0.99        32.98        13.02        35.01        28.04         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       20.98        13.94         1.02        31.00        70.03        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 
       49.97         1.94        38.96        61.97         1.45         6.05 
TCGA-CI-6624 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD 
        4.73        10.98        30.05        10.06         5.29        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 
       24.13        32.61         2.40        19.96        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
       16.41         8.61        17.46         8.45        31.30 

  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE 
                          17.41                           21.44 
[1] "0.0 - 139.2 (17.4)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   247 110
  AMP PEAK 24(20P11.21) WILD-TYPE 195  52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    247  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                            247                             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        64        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         41
  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           31       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                               64                              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                            41                              38
  STAGE IIIC                            31                              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  67 240  37
  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                            67                              40
  T3                           240                             173
  T4                            37                              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   194  95  68
  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                           194                             148
  N1                            95                              54
  N2                            68                              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"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   248  64
  AMP PEAK 24(20P11.21) WILD-TYPE 200  22
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    248   64
  AMP PEAK 24(20P11.21) WILD-TYPE  200   22
   clus
vv  AMP PEAK 24(20P11.21) MUTATED AMP PEAK 24(20P11.21) WILD-TYPE
  0                           248                             200
  1                            64                              22
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20P11.21) MUTATED   158 201
  AMP PEAK 24(20P11.21) WILD-TYPE 128 121
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED    158  201
  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                           158                             128
  MALE                             201                             121
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                    224
  AMP PEAK 24(20P11.21) WILD-TYPE                  157
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                              22
  AMP PEAK 24(20P11.21) WILD-TYPE                            38
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                     105
  AMP PEAK 24(20P11.21) WILD-TYPE                    41
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20P11.21) MUTATED                                4
  AMP PEAK 24(20P11.21) WILD-TYPE                              9
D24V9, multiclass
                                clus
vv                               AMP PEAK 24(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                     224
  COLON MUCINOUS ADENOCARCINOMA                             22
  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     7 352
  AMP PEAK 24(20P11.21) WILD-TYPE   2 247
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20P11.21) MUTATED      7  352
  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                           352                             247
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 24(20P11.21) MUTATED   257   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                           257                             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                          33   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                                   33
  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   359  85
  AMP PEAK 25(20Q11.21) WILD-TYPE 109  30
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                            444                             139 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                             85                              30 
$`AMP PEAK 25(20Q11.21) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
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        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 
       58.03         6.97         1.02        38.99         9.07        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.05         2.01        14.01        50.04        47.05 
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-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        85.05        10.06        35.05         0.99        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       10.06        33.07        32.05         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       17.03        24.03        27.02        18.05        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-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-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
        7.96        13.94        19.00        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       31.00         1.02        33.04        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 
       39.98        40.96         0.07        21.37         4.21         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         5.79        22.42        27.42         0.20        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
       17.26        17.85        19.33        18.84        75.25         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-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       17.56       102.44        40.34        49.08        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        25.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        16.01         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       11.01        11.08        11.08        11.01        10.06        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       12.26        19.59        13.51        11.51        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04        11.64        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
        6.12        14.04        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        29.59        16.24        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       65.85        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 
       36.72        36.00        26.43        26.04        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        47.15        18.18        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        9.70        30.28        24.13        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-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        36.03        20.05        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        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        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        10.98 
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        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         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 
       11.47        46.65        42.90        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        19.04         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 
       15.95         0.00         0.00        36.03        53.00        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R 
       25.02        27.02        38.04        30.02        18.05         0.99 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       34.98        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       22.03        18.05        56.55        10.88         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       21.44        17.82        50.37        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
       61.41         6.77       100.01        11.74         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
        0.10        70.16        15.62        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 
      124.27        23.05        26.04        27.02        15.02        12.00 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.95        13.05        12.03        20.42        16.14        15.58 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 
        9.44         1.51        12.00       140.38       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 
       81.37        60.79        98.24        11.11        35.87        16.31 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       19.43        74.56        67.30        53.62        51.75        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       35.80        26.17        52.80        10.98        19.33         9.93 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
       31.30        70.03        13.55        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-CI-6620 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       61.97         6.05         5.29        19.96         8.61        17.46 
TCGA-EI-7004 
        8.45 

  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE 
                         18.215                          21.140 
[1] "0.0 - 139.2 (18.2)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1"  
D25V2, continuous
D25V3, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   316 144
  AMP PEAK 25(20Q11.21) WILD-TYPE 126  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    316  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                            316                             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        79        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         63
  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           45       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                               79                              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                            63                              16
  STAGE IIIC                            45                               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  86 316  45
  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                            86                              21
  T3                           316                              97
  T4                            45                              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   240 127  93
  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                           240                             102
  N1                           127                              22
  N2                            93                              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"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   331  76
  AMP PEAK 25(20Q11.21) WILD-TYPE 117  10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    331   76
  AMP PEAK 25(20Q11.21) WILD-TYPE  117   10
   clus
vv  AMP PEAK 25(20Q11.21) MUTATED AMP PEAK 25(20Q11.21) WILD-TYPE
  0                           331                             117
  1                            76                              10
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q11.21) MUTATED   212 251
  AMP PEAK 25(20Q11.21) WILD-TYPE  74  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED    212  251
  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                           212                              74
  MALE                             251                              71
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                    289
  AMP PEAK 25(20Q11.21) WILD-TYPE                   92
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q11.21) MUTATED                              26
  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                                     289
  COLON MUCINOUS ADENOCARCINOMA                             26
  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     8 455
  AMP PEAK 25(20Q11.21) WILD-TYPE   1 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q11.21) MUTATED      8  455
  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                           455                             144
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 25(20Q11.21) MUTATED   332   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                           332                             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                          44   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                                   44
  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   361  85
  AMP PEAK 26(20Q12) WILD-TYPE 107  30
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                         446                          137 
  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                          85                           30 
$`AMP PEAK 26(20Q12) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
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        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 
       58.03         6.97         1.02        38.99         9.07        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.05         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        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        10.06        35.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       33.07        32.05         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 
       24.03        27.02        18.05        12.99        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       13.94        19.00        34.03        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
       15.02        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42         0.20        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D 
       16.31         0.95        15.75         0.20        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 
       19.33        18.84        75.25         1.41         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
      102.44        40.34        49.08        21.99         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        11.64        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
       14.04        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
        8.61        13.38        13.64        13.45         6.18         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        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       74.56        65.85        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        36.00        26.43        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       91.79        46.75        47.15        18.18        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        8.42         9.70        30.28        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-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        36.03        20.05        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 
       26.43         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        78.12         7.17        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        10.98        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        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         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 
       11.47        46.65        42.90        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        19.04         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        2.01        25.02        27.02        38.04        30.02        18.05 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        34.98        10.98        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
       35.01        39.06        22.03        18.05        56.55        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
        0.92        27.09        21.44        17.82        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 
       32.94        61.41         6.77       100.01        11.74         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.33         0.10        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
        2.93       124.27        23.05        26.04        27.02        15.02 
TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 
       12.00        12.95        13.05        12.03        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB 
       15.58         9.44         1.51        12.00       140.38       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 
        7.76        81.37        60.79        98.24        11.11        35.87 
TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 
       19.43        67.30        53.62        51.75        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       26.17        52.80        10.98        19.33         9.93        31.30 
TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 
       70.03        13.55        12.72        12.00        32.02         2.01 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N 
        6.05        32.98        13.02        20.98        49.97        61.97 
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 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE 
                           0                            0 
  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 
                      18.215                       21.140 
[1] "0.0 - 139.2 (18.2)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1"  
D26V2, continuous
D26V3, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   317 145
  AMP PEAK 26(20Q12) WILD-TYPE 125  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    317  145
  AMP PEAK 26(20Q12) WILD-TYPE  125   17
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  COLON                         317                          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        79        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         63
  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           45       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                            79                           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                         63                           16
  STAGE IIIC                         45                            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  86 317  46
  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                         86                           21
  T3                        317                           96
  T4                         46                           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   241 128  93
  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                        241                          101
  N1                        128                           21
  N2                         93                           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"
D26V7, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   331  78
  AMP PEAK 26(20Q12) WILD-TYPE 117   8
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    331   78
  AMP PEAK 26(20Q12) WILD-TYPE  117    8
   clus
vv  AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  0                        331                          117
  1                         78                            8
[1] 2 2
[1] FALSE
D26V8, binary
                              cls
clus                             0   1
  AMP PEAK 26(20Q12) MUTATED   213 252
  AMP PEAK 26(20Q12) WILD-TYPE  73  70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED    213  252
  AMP PEAK 26(20Q12) WILD-TYPE   73   70
        clus
vv       AMP PEAK 26(20Q12) MUTATED AMP PEAK 26(20Q12) WILD-TYPE
  FEMALE                        213                           73
  MALE                          252                           70
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                    291
  AMP PEAK 26(20Q12) WILD-TYPE                   90
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q12) MUTATED                              25
  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                                  291
  COLON MUCINOUS ADENOCARCINOMA                          25
  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     8 457
  AMP PEAK 26(20Q12) WILD-TYPE   1 142
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 26(20Q12) MUTATED      8  457
  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                        457                          142
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 26(20Q12) MUTATED   333   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                        333                          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                          44   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                                44
  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   363  86
  AMP PEAK 27(20Q13.31) WILD-TYPE 105  29
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                            449                             134 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                             86                              29 
$`AMP PEAK 27(20Q13.31) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
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        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 
       58.03         6.97         1.02        38.99         9.07        36.03 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       36.00         5.03        85.05        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       25.02        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
       31.07        17.03        24.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       19.07         7.96        13.94        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        15.02        15.02        10.98        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-A5EK 
        0.79         0.72         5.79        22.42        27.42        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        15.75         0.20 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
       17.26        17.85        19.33        18.84        75.25         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-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         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        49.08        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        2.01        20.02        37.02        25.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        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 
       45.40        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        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        17.13        12.49         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.43        14.30         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-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 
       13.25         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        65.85        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        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        15.65        12.79        13.05        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       29.46        32.98         8.42         9.70        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-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 
       36.03        20.05        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        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         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 
       78.12         7.17        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        10.98        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        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        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 
       11.47        46.65        42.90        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        19.04         1.02        17.98        15.95 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 
        0.00         0.00        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-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R 
       38.07         1.02        35.01        35.01        39.06        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
       18.05        56.55        10.88         0.20         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       21.44        17.82        50.37        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       61.41         6.77       100.01         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        67.30 
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-3400 
       10.98        19.33         9.93        31.30        70.03        12.72 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 
       12.00        32.02         2.01         6.05        32.98        13.02 
TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
       20.98        49.97        61.97         5.29        19.96         8.61 
TCGA-EI-6917 TCGA-EI-7004 
       17.46         8.45 

  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                              0                               0 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE 
                          18.18                           21.29 
[1] "0.0 - 139.2 (18.2)" "0.0 - 140.4 (21.3)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   319 145
  AMP PEAK 27(20Q13.31) WILD-TYPE 123  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    319  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                            319                             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        79        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         63
  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           46       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                               79                              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                            63                              16
  STAGE IIIC                            46                               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  86 321  45
  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                            86                              21
  T3                           321                              92
  T4                            45                              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   243 128  94
  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                           243                              99
  N1                           128                              21
  N2                            94                              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"
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   335  78
  AMP PEAK 27(20Q13.31) WILD-TYPE 113   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    335   78
  AMP PEAK 27(20Q13.31) WILD-TYPE  113    8
   clus
vv  AMP PEAK 27(20Q13.31) MUTATED AMP PEAK 27(20Q13.31) WILD-TYPE
  0                           335                             113
  1                            78                               8
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.31) MUTATED   216 252
  AMP PEAK 27(20Q13.31) WILD-TYPE  70  70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED    216  252
  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                           216                              70
  MALE                             252                              70
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                    292
  AMP PEAK 27(20Q13.31) WILD-TYPE                   89
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(20Q13.31) MUTATED                              26
  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                                     292
  COLON MUCINOUS ADENOCARCINOMA                             26
  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     8 460
  AMP PEAK 27(20Q13.31) WILD-TYPE   1 139
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.31) MUTATED      8  460
  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                           460                             139
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 27(20Q13.31) MUTATED   336   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                           336                             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                          44   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                                   44
  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   178  52
  DEL PEAK  1(1P36.11) WILD-TYPE 290  63
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           230                            353 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            52                             63 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
        4.80        43.76        24.33        44.91        35.11        13.94 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 
       16.57        36.53        14.53        32.45        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 
       32.71        29.16        22.52        24.13        25.18        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       23.87        56.25         5.03        38.99         9.07        37.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3553 
       19.07        19.07        34.03        14.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       23.01        19.99         2.01        14.01        50.04        47.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 
       37.05        19.00        36.00        85.05        10.06        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       38.99        36.95        37.02        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
        0.99        31.07        31.07        17.03        24.03        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-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 
       13.05        26.01         7.96        34.03        42.02        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-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 
       39.98         2.01         5.03        41.00        40.96         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        5.79        22.42         0.20        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       16.31        17.85         5.65         5.13        22.36        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 
        2.14         3.29         0.07         0.26         1.35        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 
        2.01        25.02         8.02        13.02        22.03        30.08 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        5.03        15.02        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 
       11.01        11.08        10.06        12.03        45.40        13.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        17.75         1.32        43.27        15.12        17.85 
TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
       15.58        12.43        14.30        13.41        11.38        92.75 
TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28H 
       49.91        44.32       139.17         6.12        26.47       117.07 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 
       95.18        13.38        11.11         1.55        29.59        13.25 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 
       35.41         8.35        82.39        23.51        65.85        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       36.72        36.00        91.79        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
        9.93        12.00        42.77        24.13        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K 
       13.55        19.10        10.39        14.50        15.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       65.98        11.84        32.02        36.03        20.05        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
       46.03        34.03         6.05        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        1.02        19.99         1.02        36.95        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H 
       48.03        19.99        28.04        36.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       23.01        12.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.96        38.04         0.49         0.69         0.72        10.19 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        6.97         4.73        11.01        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00        30.05        12.95        10.06       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 
      129.27        32.61         0.49         2.40        20.55        15.85 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 
       11.97         8.45        28.57        32.19         0.69         0.46 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47        11.47        43.76        46.65        43.43        42.90 
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        37.02        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         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 
       13.02         1.02        24.03        36.03         8.05         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
       29.00        29.00        26.01        12.99         0.99        33.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-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-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 
       15.95        14.93         0.00        17.03         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       36.03        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00        20.98        34.03        16.08 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       34.06        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       21.99        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       21.37         4.21        56.55         0.72        27.42        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        19.33        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41        32.94        83.80        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 
       49.41         6.77       100.01        11.74         1.94         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        49.08        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-5341 
       23.05        20.02        37.02        26.04        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.98        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-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 
       12.95        13.05        11.08        11.01        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       11.51        20.42        18.25         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 
       16.14         7.53        12.39        10.13         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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
       35.97        60.79        98.24         8.61        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
        6.18        35.87        16.31        16.24        33.67         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       19.43       107.67        28.21        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       44.68        55.04        51.75        45.11        39.42        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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       52.80        19.33        19.33        15.65        12.79        13.05 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30         9.70        30.28 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       70.03        39.48        12.72        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 
       10.39        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 
        7.99        32.98         0.99         0.99        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-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        1.02        31.00        10.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
        1.45        26.43         1.81         6.05         6.05         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 
       13.97        78.12         7.17        10.98        15.02        10.98 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       13.05         5.29        41.36        57.24        24.13        51.48 
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-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       17.46         9.96        37.51        31.30         0.39         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        18.28        55.76 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        19.085                         19.040 
[1] "0.1 - 139.2 (19.1)" "0.0 - 140.4 (19.0)"
[1] "hr=" "1.3"
D28V2, continuous
D28V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   164  73
  DEL PEAK  1(1P36.11) WILD-TYPE 278  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    164   73
  DEL PEAK  1(1P36.11) WILD-TYPE  278   89
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  COLON                           164                            278
  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      71        1       28       109         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1        10          7         30
  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         28       24        11         2
D28V4, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              33                             71
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            62                            109
  STAGE IIB                             3                              7
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            7                             14
  STAGE IIIB                           30                             49
  STAGE IIIC                           26                             28
  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  32
  DEL PEAK  1(1P36.11) WILD-TYPE  15  67 251  34
D28V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            5                             15
  T2                           40                             67
  T3                          162                            251
  T4                           32                             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   115  65  58
  DEL PEAK  1(1P36.11) WILD-TYPE 227  84  56
D28V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          115                            227
  N1                           65                             84
  N2                           58                             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"
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   161  52
  DEL PEAK  1(1P36.11) WILD-TYPE 287  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    161   52
  DEL PEAK  1(1P36.11) WILD-TYPE  287   34
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          161                            287
  1                           52                             34
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   104 136
  DEL PEAK  1(1P36.11) WILD-TYPE 182 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    104  136
  DEL PEAK  1(1P36.11) WILD-TYPE  182  186
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                          104                            182
  MALE                            136                            186
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                    152
  DEL PEAK  1(1P36.11) WILD-TYPE                  229
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              11
  DEL PEAK  1(1P36.11) WILD-TYPE                            49
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                      65
  DEL PEAK  1(1P36.11) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                7
  DEL PEAK  1(1P36.11) WILD-TYPE                              6
D28V9, multiclass
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                    152
  COLON MUCINOUS ADENOCARCINOMA                            11
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      229
  COLON MUCINOUS ADENOCARCINOMA                              49
  RECTAL ADENOCARCINOMA                                      81
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     4 236
  DEL PEAK  1(1P36.11) WILD-TYPE   5 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      4  236
  DEL PEAK  1(1P36.11) WILD-TYPE    5  363
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             4                              5
  YES                          236                            363
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   163   2  21  12
  DEL PEAK  1(1P36.11) WILD-TYPE 276   3  15  17
D28V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          163                            276
  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                          22   115
  DEL PEAK  1(1P36.11) WILD-TYPE                        38   177
D28V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     115
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    38
  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   125  41
  DEL PEAK  2(1P33) WILD-TYPE 343  74
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        166                         417 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         41                          74 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
        4.80        43.76        35.11        16.57        37.25        37.02 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 
       36.53        14.53        32.45        29.19        23.61        29.16 
TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       22.52        21.76        23.87         5.03        38.99         9.07 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 
       37.05         8.05        21.01        19.99        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       19.00        85.05        10.06        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 
        0.00        10.06        33.07        32.05        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       24.03         2.01        12.99         2.01        21.99        13.05 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
        7.96        34.03        42.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W 
       33.04        26.01         2.96         2.01        22.03        41.00 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        0.79         5.79        22.42         0.20        16.44        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 
       16.31        17.85         5.65         5.13        62.79        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19         2.24         3.06         2.14 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 
        0.26         2.01         8.02        13.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.08        10.06        13.51         1.32        15.12        17.85 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       14.30        13.41        11.38        38.20        92.75        49.91 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 
       14.04        26.47        35.97        13.38         1.55        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        65.85        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        18.18        10.98         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 
       12.00        42.77        24.13        17.23        13.55        14.50 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       15.39        86.63        65.98        11.84        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 
       24.00        34.03        29.98         1.02        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y 
       48.03        19.99        28.04        36.03        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       12.00        70.03         1.94        38.96        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        0.69        10.19         9.37         4.73        13.97        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       11.01        12.99        13.97        36.00        30.05       126.44 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 
      129.27         0.49        20.55        15.85        13.64        11.97 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       28.57        32.19         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 
       11.47        11.47        43.76        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       24.33        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-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-3529 TCGA-AA-3530 
        1.02        24.03        36.03        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-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-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-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 
       25.02         1.02        17.98        15.95        14.93        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       27.02        29.98        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-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-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       50.99        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        38.04         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.03        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J 
       35.01        37.02        39.06        51.98        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
        0.92        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
        4.21        56.55         0.72        27.42        10.88         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        19.33        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       61.41        49.41         6.77       100.01        11.74         1.94 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       20.02        37.02        25.02        26.04        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        16.01        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        12.26        19.59        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        43.27         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        24.43       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        16.24        33.67        13.25 
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        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       13.05        29.46        32.98         8.42        31.30         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       30.28        70.03        39.48        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        16.83        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        20.05         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        26.43 
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        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02        10.98        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                           0 
  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 
                     18.015                      19.100 
[1] "0.0 - 129.3 (18.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   120  51
  DEL PEAK  2(1P33) WILD-TYPE 322 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    120   51
  DEL PEAK  2(1P33) WILD-TYPE  322  111
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  COLON                        120                         322
  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      85        1       29       122         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         7          5         25
  DEL PEAK  2(1P33) WILD-TYPE         3        19         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         34       33        21         2
D29V4, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           19                          85
  STAGE IA                           0                           1
  STAGE II                           7                          29
  STAGE IIA                         49                         122
  STAGE IIB                          1                           9
  STAGE IIC                          0                           3
  STAGE III                          7                          19
  STAGE IIIA                         5                          16
  STAGE IIIB                        25                          54
  STAGE IIIC                        20                          34
  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  21
  DEL PEAK  2(1P33) WILD-TYPE  16  84 289  45
D29V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         4                          16
  T2                        23                          84
  T3                       124                         289
  T4                        21                          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  51  39
  DEL PEAK  2(1P33) WILD-TYPE 260  98  75
D29V6, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        82                         260
  N1                        51                          98
  N2                        39                          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"
D29V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   117  34
  DEL PEAK  2(1P33) WILD-TYPE 331  52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    117   34
  DEL PEAK  2(1P33) WILD-TYPE  331   52
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                       117                         331
  1                        34                          52
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    78  95
  DEL PEAK  2(1P33) WILD-TYPE 208 227
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     78   95
  DEL PEAK  2(1P33) WILD-TYPE  208  227
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        78                         208
  MALE                          95                         227
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                    110
  DEL PEAK  2(1P33) WILD-TYPE                  271
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                              10
  DEL PEAK  2(1P33) WILD-TYPE                            50
                             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                                 110
  COLON MUCINOUS ADENOCARCINOMA                         10
  RECTAL ADENOCARCINOMA                                 49
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                   271
  COLON MUCINOUS ADENOCARCINOMA                           50
  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     3 170
  DEL PEAK  2(1P33) WILD-TYPE   6 429
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3  170
  DEL PEAK  2(1P33) WILD-TYPE    6  429
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          3                           6
  YES                       170                         429
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED   114   2  14   8
  DEL PEAK  2(1P33) WILD-TYPE 325   3  22  21
D29V11, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                       114                         325
  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                          21    83
  DEL PEAK  2(1P33) WILD-TYPE                        39   209
D29V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               21
  WHITE                                                   83
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 39
  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   126  39
  DEL PEAK  3(1P13.2) WILD-TYPE 342  76
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          165                           418 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           39                            76 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
        4.80        43.76        43.76        35.11        16.57        37.25 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       36.53        14.53        32.45        29.19        23.61        22.52 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       21.76        23.87        56.25         5.03        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 
       24.03        37.05        21.01        13.94        19.99        50.04 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 
       37.05        19.00        10.06        38.99        37.02        10.06 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 
       32.05        31.07        17.03        24.03         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A 
        2.01         2.01        21.99        13.05         7.96        38.04 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T 
       42.02        15.02        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 
       26.01         2.96         2.01        41.00        40.96         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 
        5.79        22.42         0.20        16.44         0.92        14.50 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 
       17.85         5.65        32.94         5.13        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-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6163 
        0.26         2.01         8.02        13.02        22.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 
       29.03        13.02        15.02        11.08        10.06        13.51 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 
       17.75         1.32        15.12        14.30        13.41        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       92.75        49.91       131.51         6.12        14.04        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 
       13.38         1.55        16.24        33.67        35.41         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       82.39        23.51        65.85        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        18.18        10.98         9.93        12.00        42.77 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       24.13        17.23        13.55        14.50        15.39        65.98 
TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 
       11.84        32.02        36.03        24.00        34.03         2.01 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
       29.98         1.02        19.99         1.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 
       36.03        25.97        23.01        12.00        70.03         1.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-DC-4749 
       38.04         0.49         0.69        10.19         9.37        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.99        13.97        36.00        30.05       126.44        41.36 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 
      129.27         0.49        20.55        17.00        15.85        11.51 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       13.64        11.97        28.57        32.19         0.66         0.69 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.76        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 
       11.47        11.47        46.65        43.43        42.90        24.33 
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        37.02 
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         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
        1.02        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-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-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        10.98        12.00        31.00        38.07        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-A02Y TCGA-AA-A03F TCGA-AD-5900 
        5.03         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       21.37         4.21        56.55         0.72        27.42        10.88 
TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       50.37        58.39         1.41        83.80        22.36        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-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        49.08 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       20.02        37.02        25.02        26.04        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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-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-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        20.42        18.25        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65         7.76       139.17        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-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 
       13.25         0.53        19.43       107.67        28.21        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        12.79        13.05        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 
       31.30         9.70        30.28        70.03        39.48        43.04 
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        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       10.39        86.63        36.03        12.00         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       20.05         1.02        46.03        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-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-3898 TCGA-AG-3902 TCGA-AG-4005 
       13.02        35.01        14.01        48.03        32.02        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         1.45         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         4.73        13.97        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       10.98        15.02        12.00        15.02        10.98        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       13.05        10.06         5.29        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
       32.61         2.40        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.31        16.41         8.61        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 
        8.45         9.96        37.51        31.30         0.39         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        1.12         0.46        55.76        26.43 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                        17.23                         19.38 
[1] "0.2 - 131.5 (17.2)" "0.0 - 140.4 (19.4)"
[1] "hr=" "1.5"
D30V2, continuous
D30V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   118  52
  DEL PEAK  3(1P13.2) WILD-TYPE 324 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    118   52
  DEL PEAK  3(1P13.2) WILD-TYPE  324  110
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  COLON                          118                           324
  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      85        1       28       124         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.2) MUTATED           2         5          4         24
  DEL PEAK  3(1P13.2) WILD-TYPE         1        21         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         33       32        21         2
D30V4, multiclass
            clus
vv           DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  STAGE I                             19                            85
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           47                           124
  STAGE IIB                            1                             9
  STAGE IIC                            2                             1
  STAGE III                            5                            21
  STAGE IIIA                           4                            17
  STAGE IIIB                          24                            55
  STAGE IIIC                          21                            33
  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  22
  DEL PEAK  3(1P13.2) WILD-TYPE  15  86 290  44
D30V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           5                            15
  T2                          21                            86
  T3                         123                           290
  T4                          22                            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  46  44
  DEL PEAK  3(1P13.2) WILD-TYPE 261 103  70
D30V6, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          81                           261
  N1                          46                           103
  N2                          44                            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"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   118  35
  DEL PEAK  3(1P13.2) WILD-TYPE 330  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    118   35
  DEL PEAK  3(1P13.2) WILD-TYPE  330   51
   clus
vv  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  0                         118                           330
  1                          35                            51
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED    77  95
  DEL PEAK  3(1P13.2) WILD-TYPE 209 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     77   95
  DEL PEAK  3(1P13.2) WILD-TYPE  209  227
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          77                           209
  MALE                            95                           227
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                    108
  DEL PEAK  3(1P13.2) WILD-TYPE                  273
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                              10
  DEL PEAK  3(1P13.2) WILD-TYPE                            50
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                      49
  DEL PEAK  3(1P13.2) WILD-TYPE                    97
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                                2
  DEL PEAK  3(1P13.2) WILD-TYPE                             11
D30V9, multiclass
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  COLON ADENOCARCINOMA                                   108
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     273
  COLON MUCINOUS ADENOCARCINOMA                             50
  RECTAL ADENOCARCINOMA                                     97
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     4 168
  DEL PEAK  3(1P13.2) WILD-TYPE   5 431
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      4  168
  DEL PEAK  3(1P13.2) WILD-TYPE    5  431
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                            4                             5
  YES                         168                           431
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.2) MUTATED   115   1  14   9
  DEL PEAK  3(1P13.2) WILD-TYPE 324   4  22  20
D30V11, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                         115                           324
  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                          20    85
  DEL PEAK  3(1P13.2) WILD-TYPE                        40   207
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                     85
                                  clus
vv                                 DEL PEAK  3(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   40
  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 452 112
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         19                         564 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          3                         112 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-A6-2677 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 TCGA-AA-A01S 
       24.33         6.97        19.99        37.02        12.99         1.02 
TCGA-CM-5341 TCGA-G4-6626 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       29.06        46.75        15.39        32.02        36.03         6.05 
TCGA-AG-3609 TCGA-AG-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-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        42.90        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.18        24.16        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-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-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        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.00        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       27.42        10.88         0.20        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
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 
       49.08        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        25.02        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        45.40        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        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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        13.25         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        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       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        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30         9.70 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-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-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         8.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-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-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         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        78.12         7.17 
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-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        37.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      46.75                      140.38 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      24.33                       19.04 
[1] "1.0 - 46.8 (24.3)"  "0.0 - 140.4 (19.0)"
[1] "hr=" "1.1"
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8  13
  DEL PEAK  4(2P12) WILD-TYPE 434 149
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   13
  DEL PEAK  4(2P12) WILD-TYPE  434  149
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  COLON                          8                         434
  RECTUM                        13                         149
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  4(2P12) MUTATED         2        0        1         7         0
  DEL PEAK  4(2P12) WILD-TYPE     102        1       35       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         78
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(2P12) MUTATED            5        1         1         0
  DEL PEAK  4(2P12) WILD-TYPE         49       60        26         2
D31V4, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                         102
  STAGE IA                           0                           1
  STAGE II                           1                          35
  STAGE IIA                          7                         164
  STAGE IIB                          0                          10
  STAGE IIC                          0                           3
  STAGE III                          1                          25
  STAGE IIIA                         2                          19
  STAGE IIIB                         1                          78
  STAGE IIIC                         5                          49
  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  20 103 398  64
D31V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                          20
  T2                         4                         103
  T3                        15                         398
  T4                         2                          64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK  4(2P12) MUTATED    10   5   6
  DEL PEAK  4(2P12) WILD-TYPE 332 144 108
D31V6, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        10                         332
  N1                         5                         144
  N2                         6                         108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    18   2
  DEL PEAK  4(2P12) WILD-TYPE 430  84
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     18    2
  DEL PEAK  4(2P12) WILD-TYPE  430   84
   clus
vv  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  0                        18                         430
  1                         2                          84
[1] 2 2
[1] FALSE
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11  10
  DEL PEAK  4(2P12) WILD-TYPE 275 312
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11   10
  DEL PEAK  4(2P12) WILD-TYPE  275  312
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                        11                         275
  MALE                          10                         312
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      8
  DEL PEAK  4(2P12) WILD-TYPE                  373
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                               0
  DEL PEAK  4(2P12) WILD-TYPE                            60
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      11
  DEL PEAK  4(2P12) WILD-TYPE                   135
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                                1
  DEL PEAK  4(2P12) WILD-TYPE                             12
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                                   373
  COLON MUCINOUS ADENOCARCINOMA                           60
  RECTAL ADENOCARCINOMA                                  135
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     1  20
  DEL PEAK  4(2P12) WILD-TYPE   8 579
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      1   20
  DEL PEAK  4(2P12) WILD-TYPE    8  579
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          1                           8
  YES                        20                         579
[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 421   5  35  29
D31V11, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        18                         421
  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                        60   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                                 60
  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 443 108
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           32                           551 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                           108 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3522 
       42.28        36.53        21.76        24.92         6.97        37.05 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3848 
       19.99         2.01        15.02        10.06        37.02        10.06 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AZ-4308 TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 
       12.99        24.00        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        42.90        24.33        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-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-3561 
       24.00        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        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        19.04        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        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         5.79        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84        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        49.08        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        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        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        45.40        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        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        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 
       13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30         9.70        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        19.10        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        16.83        15.39        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-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-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-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-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-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       17.03         0.99        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         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        78.12         7.17 
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-6683 
       15.02        36.00        10.98        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        37.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19         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  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         0.53                          0.00 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                        24.46                         19.00 
[1] "0.5 - 131.5 (24.5)" "0.0 - 140.4 (19.0)"
[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 418 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     24   11
  DEL PEAK  5(2Q22.1) WILD-TYPE  418  151
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON                           24                           418
  RECTUM                          11                           151
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  5(2Q22.1) MUTATED         2        0        1        15         0
  DEL PEAK  5(2Q22.1) WILD-TYPE     102        1       35       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         75
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED            7        2         1         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         47       59        26         2
D32V4, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              2                           102
  STAGE IA                             0                             1
  STAGE II                             1                            35
  STAGE IIA                           15                           156
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           1                            20
  STAGE IIIB                           4                            75
  STAGE IIIC                           7                            47
  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  20 103 386  62
D32V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           103
  T3                          27                           386
  T4                           4                            62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  5(2Q22.1) MUTATED    18   8   9
  DEL PEAK  5(2Q22.1) WILD-TYPE 324 141 105
D32V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          18                           324
  N1                           8                           141
  N2                           9                           105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    30   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 418  83
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     30    3
  DEL PEAK  5(2Q22.1) WILD-TYPE  418   83
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          30                           418
  1                           3                            83
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    15  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 271 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     15   20
  DEL PEAK  5(2Q22.1) WILD-TYPE  271  302
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          15                           271
  MALE                            20                           302
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                     21
  DEL PEAK  5(2Q22.1) WILD-TYPE                  360
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                               3
  DEL PEAK  5(2Q22.1) WILD-TYPE                            57
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                      10
  DEL PEAK  5(2Q22.1) WILD-TYPE                   136
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                0
  DEL PEAK  5(2Q22.1) WILD-TYPE                             13
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                                     360
  COLON MUCINOUS ADENOCARCINOMA                             57
  RECTAL ADENOCARCINOMA                                    136
  RECTAL MUCINOUS ADENOCARCINOMA                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  35
  DEL PEAK  5(2Q22.1) WILD-TYPE   9 564
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   35
  DEL PEAK  5(2Q22.1) WILD-TYPE    9  564
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                            0                             9
  YES                          35                           564
[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 414   5  34  27
D32V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          25                           414
  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                        58   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                                   58
  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    68  18
  DEL PEAK  6(3P26.3) WILD-TYPE 400  97
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           86                           497 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           18                            97 
$`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        16.57        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        10.06        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        16.44         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        43.27        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         9.93        42.77 
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        20.05        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 
       13.94        37.05        37.25        37.02        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        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-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3663 TCGA-AA-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-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       36.95        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        24.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88         0.20         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.85        19.33        18.84        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        49.08        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 
       25.02        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        45.40        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         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 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 
       13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        13.05        12.00        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30         9.70        70.03        24.13        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       43.04        19.10        37.74        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 
       12.00        32.02         8.02         7.07        36.03         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-3728 
        0.99        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99         0.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.94        38.96        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        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        10.98 
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-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                        13.99                         19.99 
[1] "0.2 - 85.0 (14.0)"  "0.0 - 140.4 (20.0)"
[1] "hr=" "1.7"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    68  20
  DEL PEAK  6(3P26.3) WILD-TYPE 374 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     68   20
  DEL PEAK  6(3P26.3) WILD-TYPE  374  142
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  COLON                           68                           374
  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      96        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         65
                               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         46       42        22         2
D33V4, multiclass
            clus
vv           DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  STAGE I                              8                            96
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           24                           147
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           2                            19
  STAGE IIIB                          14                            65
  STAGE IIIC                           8                            46
  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  99 344  55
D33V5, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  T1                           2                            18
  T2                           8                            99
  T3                          69                           344
  T4                          11                            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  6(3P26.3) MUTATED    38  28  24
  DEL PEAK  6(3P26.3) WILD-TYPE 304 121  90
D33V6, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  N0                          38                           304
  N1                          28                           121
  N2                          24                            90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    55  24
  DEL PEAK  6(3P26.3) WILD-TYPE 393  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     55   24
  DEL PEAK  6(3P26.3) WILD-TYPE  393   62
   clus
vv  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  0                          55                           393
  1                          24                            62
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    40  50
  DEL PEAK  6(3P26.3) WILD-TYPE 246 272
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     40   50
  DEL PEAK  6(3P26.3) WILD-TYPE  246  272
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  FEMALE                          40                           246
  MALE                            50                           272
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                     64
  DEL PEAK  6(3P26.3) WILD-TYPE                  317
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                               4
  DEL PEAK  6(3P26.3) WILD-TYPE                            56
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                      16
  DEL PEAK  6(3P26.3) WILD-TYPE                   130
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                                3
  DEL PEAK  6(3P26.3) WILD-TYPE                             10
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                                     317
  COLON MUCINOUS ADENOCARCINOMA                             56
  RECTAL ADENOCARCINOMA                                    130
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED     2  88
  DEL PEAK  6(3P26.3) WILD-TYPE   7 511
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED      2   88
  DEL PEAK  6(3P26.3) WILD-TYPE    7  511
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  NO                            2                             7
  YES                          88                           511
[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 378   5  25  24
D33V11, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  R0                          61                           378
  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                        53   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                                   53
  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    88  22
  DEL PEAK  7(3P14.2) WILD-TYPE 380  93
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          110                           473 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           22                            93 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-4T-AA8H TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       11.47        16.57        37.02        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 
       56.25         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 
       10.06        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        38.04        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         5.79        16.44         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        43.27        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         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2693 
       12.00        42.77        30.28        70.03        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 
       20.05        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        10.98        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-4N-A93T TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       13.94        37.05        37.25        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-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        23.87        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92        61.84         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-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-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-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       26.01        25.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00U 
       30.02        34.03        18.05         4.01        42.02        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        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-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-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05        40.96         0.07         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        0.72        22.42        27.42        10.88         0.20         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        15.75        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84        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        49.08        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        25.02        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        45.40        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 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-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 
       13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       13.05        29.46        32.98         8.42        31.30         9.70 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-3913 
       24.13        39.48        17.23        13.55        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       16.83        15.39        20.02        10.39        65.98        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       12.00        32.02        36.03         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
       19.99        19.99         7.99         0.99        29.98         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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H 
       36.03        14.04         0.99        20.98        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72        26.43         1.81         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       12.99        12.00        13.97        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       119.70                        140.38 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       14.515                        19.990 
[1] "0.2 - 119.7 (14.5)" "0.0 - 140.4 (20.0)"
[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 357 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     85   29
  DEL PEAK  7(3P14.2) WILD-TYPE  357  133
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  COLON                           85                           357
  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      85        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         61
                               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         43       44        21         1
D34V4, multiclass
            clus
vv           DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  STAGE I                             19                            85
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           32                           139
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           1                            20
  STAGE IIIB                          18                            61
  STAGE IIIC                          11                            43
  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  92 335  50
D34V5, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                           7                            13
  T2                          15                            92
  T3                          78                           335
  T4                          16                            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  7(3P14.2) MUTATED    58  31  27
  DEL PEAK  7(3P14.2) WILD-TYPE 284 118  87
D34V6, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                          58                           284
  N1                          31                           118
  N2                          27                            87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    76  24
  DEL PEAK  7(3P14.2) WILD-TYPE 372  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     76   24
  DEL PEAK  7(3P14.2) WILD-TYPE  372   62
   clus
vv  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  0                          76                           372
  1                          24                            62
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    51  65
  DEL PEAK  7(3P14.2) WILD-TYPE 235 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     51   65
  DEL PEAK  7(3P14.2) WILD-TYPE  235  257
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                          51                           235
  MALE                            65                           257
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                     76
  DEL PEAK  7(3P14.2) WILD-TYPE                  305
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                               9
  DEL PEAK  7(3P14.2) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                      25
  DEL PEAK  7(3P14.2) WILD-TYPE                   121
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                                3
  DEL PEAK  7(3P14.2) WILD-TYPE                             10
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                                     305
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                    121
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED     2 114
  DEL PEAK  7(3P14.2) WILD-TYPE   7 485
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      2  114
  DEL PEAK  7(3P14.2) WILD-TYPE    7  485
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  NO                            2                             7
  YES                         114                           485
[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 359   4  25  24
D34V11, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  R0                          80                           359
  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                        46   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                                   46
  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  13
  DEL PEAK  8(3Q26.31) WILD-TYPE 419 102
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            62                            521 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            13                            102 
$`DEL PEAK  8(3Q26.31) MUTATED`
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3529 
       16.57        37.25        14.53        32.45        38.99         0.00 
TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3939 TCGA-AA-3966 
        6.05        85.05        10.06        32.05        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01T 
       21.99         7.96        13.94        27.02        32.02        33.04 
TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6600 TCGA-CA-6716 
       21.37         5.79        16.44        15.75        12.10         0.26 
TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5540 
       13.02        15.02         5.03        11.08        11.01        13.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6931 
       20.19         1.32        43.27        17.85        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6297 TCGA-G4-6317 
       11.38         7.50       131.51        35.97        82.39        36.00 
TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 
       42.77        30.28        12.72        14.50        32.02        20.05 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A02G 
       12.03        19.99         1.02        36.03        14.04        38.96 
TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 
        6.05        13.05         5.29        19.96        20.91         8.61 
TCGA-EI-7002 TCGA-G5-6233 
       11.97        18.28 

$`DEL PEAK  8(3Q26.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.43        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       45.60        13.94        37.05        37.02        34.65        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-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-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-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07         0.00        36.03         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       41.00        39.98        18.05        40.96         0.07         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        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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-6601 TCGA-AZ-6603 
       62.79        61.41        49.41         6.77       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        2.14         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-6748 
       49.08        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        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.42        17.75        18.25        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        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-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 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 
       13.25         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       13.05        12.00        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        9.70        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       13.55        19.10        37.74        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        29.98        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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         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-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-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        78.12         7.17        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-DY-A0XA TCGA-DY-A1DC 
       10.98        30.05        12.95        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-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-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        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                             0                              0 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                        14.775                         19.430 
[1] "0.0 - 131.5 (14.8)" "0.0 - 140.4 (19.4)"
[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 398 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     44   17
  DEL PEAK  8(3Q26.31) WILD-TYPE  398  145
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON                            44                            398
  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      99        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         73
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3Q26.31) MUTATED            9       12         4         0
  DEL PEAK  8(3Q26.31) WILD-TYPE         45       49        23         2
D35V4, multiclass
            clus
vv           DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            21                            150
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             3                             23
  STAGE IIIA                            0                             21
  STAGE IIIB                            6                             73
  STAGE IIIC                            9                             45
  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  20 101 366  57
D35V5, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  T1                            0                             20
  T2                            6                            101
  T3                           47                            366
  T4                            9                             57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  8(3Q26.31) MUTATED    30  14  18
  DEL PEAK  8(3Q26.31) WILD-TYPE 312 135  96
D35V6, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  N0                           30                            312
  N1                           14                            135
  N2                           18                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    41  15
  DEL PEAK  8(3Q26.31) WILD-TYPE 407  71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     41   15
  DEL PEAK  8(3Q26.31) WILD-TYPE  407   71
   clus
vv  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  0                           41                            407
  1                           15                             71
[1] 2 2
[1] FALSE
D35V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    26  36
  DEL PEAK  8(3Q26.31) WILD-TYPE 260 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     26   36
  DEL PEAK  8(3Q26.31) WILD-TYPE  260  286
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  FEMALE                           26                            260
  MALE                             36                            286
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                     41
  DEL PEAK  8(3Q26.31) WILD-TYPE                  340
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                               3
  DEL PEAK  8(3Q26.31) WILD-TYPE                            57
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                      11
  DEL PEAK  8(3Q26.31) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                                5
  DEL PEAK  8(3Q26.31) WILD-TYPE                              8
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                                      340
  COLON MUCINOUS ADENOCARCINOMA                              57
  RECTAL ADENOCARCINOMA                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED     1  61
  DEL PEAK  8(3Q26.31) WILD-TYPE   8 538
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED      1   61
  DEL PEAK  8(3Q26.31) WILD-TYPE    8  538
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  NO                             1                              8
  YES                           61                            538
[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 392   5  31  27
D35V11, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  R0                           47                            392
  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                        53   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                                    53
  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   144  41
  DEL PEAK  9(4P16.2) WILD-TYPE 324  74
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          185                           398 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                           41                            74 
$`DEL PEAK  9(4P16.2) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
        4.80        43.76        43.76        44.91        35.11        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 
       16.57        37.05        37.02        14.53        32.45        30.44 
TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       29.16        25.18        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 
       56.25         9.63         5.03         7.04        38.99        37.05 
TCGA-AA-3531 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       34.03        12.99        21.01        13.02        19.99         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 
       54.02         2.01        50.04        15.02        36.00        85.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
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-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 
       24.03        29.98         2.01        12.99         2.01        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q 
        2.01        21.99        50.99        26.01        34.03        42.02 
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-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       39.98         2.01        41.00         5.79        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
       14.50         0.95        15.75         0.20        17.85         5.65 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 
        5.13        65.00        12.10        29.56         3.19         2.14 
TCGA-CA-5797 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        3.29        49.08         8.02        29.06        22.03        22.98 
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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        11.01        10.06        45.40        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 
       17.75        14.30         9.04        13.41        11.38        12.59 
TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 
        7.50         6.12        14.04        26.47         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 
       33.67        35.41         8.35        23.51        45.11        36.72 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV 
       91.79        46.75        18.18        10.98        12.00        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 
       29.46         9.70        24.13        17.23        43.04        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 
       37.74        14.50        15.39        10.39        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       46.03        34.03         6.05        29.98         1.02        32.98 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
        1.02        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        36.03        14.04        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6643 
       23.01        12.00        70.03        38.96        41.00         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 
       10.19         6.05         6.05         4.73        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       36.00        10.98        30.05       126.44       129.27        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 
        2.40        15.85        16.34        16.41        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
       31.30        28.57         0.39         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 
       11.47        11.47        46.65        43.43        42.90        24.33 
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-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
        0.00        19.07        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-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-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       37.05        19.00         5.03        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       15.95        14.93         0.00         0.00         0.00        36.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       24.00        34.03        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        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        16.31        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         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        25.02        26.04        27.02        13.02 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 
       11.01        12.95        13.05        11.08        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        20.42        18.25         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 
       15.58         7.53        12.39        10.13        12.43         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       44.32       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        13.38        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        13.25         0.53        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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        47.15        52.80        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.79        13.05        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       30.28        70.03        39.48        13.55        19.10        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       36.95        13.02        14.01         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
        1.94        61.97        38.04         0.49         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
       26.43         1.81         6.97         9.37        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.17        10.98        11.01        15.02        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       17.00        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 
       10.78        13.64        17.46         9.96        37.51        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE 
                       19.990                        19.055 
[1] "0.2 - 129.3 (20.0)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   132  62
  DEL PEAK  9(4P16.2) WILD-TYPE 310 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    132   62
  DEL PEAK  9(4P16.2) WILD-TYPE  310  100
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  COLON                          132                           310
  RECTUM                          62                           100
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(4P16.2) MUTATED        28        0        7        47         2
  DEL PEAK  9(4P16.2) WILD-TYPE      76        1       29       124         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(4P16.2) MUTATED           0         6          9         24
  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           24       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                             28                            76
  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                          24                            55
  STAGE IIIC                          24                            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  33 132  25
  DEL PEAK  9(4P16.2) WILD-TYPE  14  74 281  41
D36V5, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  T1                           6                            14
  T2                          33                            74
  T3                         132                           281
  T4                          25                            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  57  51
  DEL PEAK  9(4P16.2) WILD-TYPE 254  92  63
D36V6, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  N0                          88                           254
  N1                          57                            92
  N2                          51                            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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED   128  42
  DEL PEAK  9(4P16.2) WILD-TYPE 320  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED    128   42
  DEL PEAK  9(4P16.2) WILD-TYPE  320   44
   clus
vv  DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  0                         128                           320
  1                          42                            44
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.2) MUTATED    84 112
  DEL PEAK  9(4P16.2) WILD-TYPE 202 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED     84  112
  DEL PEAK  9(4P16.2) WILD-TYPE  202  210
        clus
vv       DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  FEMALE                          84                           202
  MALE                           112                           210
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                    121
  DEL PEAK  9(4P16.2) WILD-TYPE                  260
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                              11
  DEL PEAK  9(4P16.2) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                      57
  DEL PEAK  9(4P16.2) WILD-TYPE                    89
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.2) MUTATED                                4
  DEL PEAK  9(4P16.2) WILD-TYPE                              9
D36V9, multiclass
                                clus
vv                               DEL PEAK  9(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                   121
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   57
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  9(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     260
  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     9 187
  DEL PEAK  9(4P16.2) WILD-TYPE   0 412
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.2) MUTATED      9  187
  DEL PEAK  9(4P16.2) WILD-TYPE    0  412
     clus
vv    DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  NO                            9                             0
  YES                         187                           412
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P16.2) MUTATED   142   0  16   6
  DEL PEAK  9(4P16.2) WILD-TYPE 297   5  20  23
D36V11, multiclass
    clus
vv   DEL PEAK  9(4P16.2) MUTATED DEL PEAK  9(4P16.2) WILD-TYPE
  R0                         142                           297
  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                          19    91
  DEL PEAK  9(4P16.2) WILD-TYPE                        41   201
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  9(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK  9(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   41
  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   163  44
  DEL PEAK 10(4Q22.1) WILD-TYPE 305  71
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          207                           376 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           44                            71 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
        4.80        43.76        43.43        44.91        35.11        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       16.57        37.05        34.65        36.53        32.45        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 
       29.19        29.16        24.16        21.76        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 
       61.84        56.25         9.63         5.03         7.04        63.98 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 
        6.97        38.99        37.05         0.00        34.03        29.00 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 
       33.99        21.01        13.02        19.99         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3837 
       50.04        37.05        36.00        19.04        10.06        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        33.07         0.99 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       31.07        17.03         2.01         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
        2.01        21.99        50.99        26.01        24.00        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01X 
       34.03        42.02        17.03        15.02        32.02        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
        2.96        39.98        41.00         5.79        22.42         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31         0.95         0.20        17.85        18.84 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 
        5.13        83.80        65.00        12.10        29.56         2.14 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 
        3.29         1.35       102.44        49.08         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       29.06        22.03         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 
       29.03        13.02        15.02        11.01        13.05        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       11.01        45.40        13.51        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       43.27        15.12        14.30         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 
       11.38        24.43        12.59         7.50        44.32         6.12 
TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
       14.04        35.97        13.38        16.24        33.67        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 
       28.21         8.35        82.39        23.51        45.11        36.72 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 
       91.79        46.75        18.18        10.98         9.93        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 
       42.77        29.46         9.70        30.28        24.13        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-A56L TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 
       15.39        65.98        36.03        34.03         6.05        19.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       29.98        32.98         1.02         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
        6.02        25.97        23.01        12.00        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
        1.94        41.00         0.49         0.69        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
        6.05         4.73        11.01        12.99        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 
       10.98        30.05        13.05       126.44       129.27         2.40 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       20.91        17.00        15.85        16.34        16.41        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        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 
       11.47        11.47        43.76        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       42.28        45.60        37.25        37.02        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-3845 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        14.93         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 
       36.03        32.05        31.07        53.00        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       26.01        24.00        16.08        13.05        34.06        25.02 
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-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        37.02        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09        15.75        21.44        17.82        17.26        19.33 
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-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-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
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-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-5348 TCGA-CM-5349 TCGA-CM-5860 
       25.02        26.04        27.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 
       14.99        12.99        14.04        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.03        12.26        19.59        11.51        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 
        7.53        12.39        10.13        12.43         9.44        11.64 
TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        1.51        10.26       119.70        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       49.91        13.32       140.38       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        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        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        0.53        19.43       107.67        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       26.17        47.15        52.80        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       12.79        13.05        32.98         8.42        31.30        70.03 
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       39.48        10.39        16.83        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-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
        1.02         0.99         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A002 
       13.02        35.01        14.01        32.02         0.99        20.98 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       10.98        51.98        49.97        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        26.43         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        78.12         7.17        10.98        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       13.97        12.95        10.06         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       13.64        17.46         9.96        37.51         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 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                            0                             0 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        18.28                         19.33 
[1] "0.0 - 129.3 (18.3)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   144  70
  DEL PEAK 10(4Q22.1) WILD-TYPE 298  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    144   70
  DEL PEAK 10(4Q22.1) WILD-TYPE  298   92
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON                          144                           298
  RECTUM                          70                            92
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4Q22.1) MUTATED        26        0       11        57         2
  DEL PEAK 10(4Q22.1) WILD-TYPE      78        1       25       114         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4Q22.1) MUTATED           1         5          9         36
  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           28       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                             26                            78
  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                          36                            43
  STAGE IIIC                          28                            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  29 155  28
  DEL PEAK 10(4Q22.1) WILD-TYPE  14  78 258  38
D37V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                           6                            14
  T2                          29                            78
  T3                         155                           258
  T4                          28                            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  65  54
  DEL PEAK 10(4Q22.1) WILD-TYPE 243  84  60
D37V6, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                          99                           243
  N1                          65                            84
  N2                          54                            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"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   151  37
  DEL PEAK 10(4Q22.1) WILD-TYPE 297  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    151   37
  DEL PEAK 10(4Q22.1) WILD-TYPE  297   49
   clus
vv  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  0                         151                           297
  1                          37                            49
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    93 125
  DEL PEAK 10(4Q22.1) WILD-TYPE 193 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     93  125
  DEL PEAK 10(4Q22.1) WILD-TYPE  193  197
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          93                           193
  MALE                           125                           197
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                    133
  DEL PEAK 10(4Q22.1) WILD-TYPE                  248
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              11
  DEL PEAK 10(4Q22.1) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                      65
  DEL PEAK 10(4Q22.1) WILD-TYPE                    81
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                4
  DEL PEAK 10(4Q22.1) WILD-TYPE                              9
D37V9, multiclass
                                clus
vv                               DEL PEAK 10(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   133
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     248
  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     8 210
  DEL PEAK 10(4Q22.1) WILD-TYPE   1 389
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      8  210
  DEL PEAK 10(4Q22.1) WILD-TYPE    1  389
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                            8                             1
  YES                         210                           389
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED   160   2  12   8
  DEL PEAK 10(4Q22.1) WILD-TYPE 279   3  24  21
D37V11, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                         160                           279
  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                          25   109
  DEL PEAK 10(4Q22.1) WILD-TYPE                        35   183
D37V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 10(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   35
  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   172  42
  DEL PEAK 11(4Q35.1) WILD-TYPE 296  73
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          214                           369 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           42                            73 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
        4.80        43.76        43.43        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5660 
       16.57        37.05        37.25        34.65        32.45        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       29.16        22.52        24.13        24.16        20.61        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
        6.97        38.99        37.05        34.03        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3660 
       14.01        33.99        21.01        13.02        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 
        6.05        54.02         2.01        50.04        37.05        36.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       10.06        33.07        36.03         0.99        31.07        17.03 
TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L 
       50.99        26.01        24.00         7.96        34.03        38.04 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S 
       42.02        15.02        32.02        31.00        35.01         1.02 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 
       26.01         2.96        39.98         2.01        41.00        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D 
        0.20        14.50        16.31         0.95         0.20        17.85 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
       75.25         5.65         5.13        65.00        12.10        29.56 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 
        2.24         2.14         0.10         1.35        49.08         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        30.08         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       15.02        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        45.40        13.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       20.19        17.75         1.32        43.27        17.85         7.53 
TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
        9.04        13.41        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 
      131.51         6.12        14.04        26.47        13.38         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       16.24        33.67        35.41         8.35        82.39        23.51 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       45.11        36.72        91.79        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D 
        9.93        12.79        12.00        42.77        29.46         9.70 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        24.13        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       12.72        37.74        10.39        14.50        15.39        65.98 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
       36.03        46.03        34.03         6.05        19.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
       32.98         0.99         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       36.03        14.04        13.94        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       70.03        64.01        41.00         0.49         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
        6.05         6.05         4.73        11.01        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF 
       36.00        10.98        30.05       126.44       129.27        24.13 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
        2.40        17.00        15.85        16.34        16.41        11.97 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6814 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.53         0.46        18.28        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 
       11.47        11.47        43.76        46.65        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       42.28        44.91        37.02        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         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3534 
       36.03         8.05        19.07         0.00        19.07        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       12.99         0.99        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 
       20.98        19.99        13.94        61.02         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       19.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00         0.00        32.05        31.07        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3973 
       24.00        33.01        26.01        24.00         2.01        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        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-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J 
       33.04        35.01        37.02        39.06        51.98         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         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        10.88        16.44         0.46         0.92        27.09 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       15.75        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       50.37        58.39         1.41        32.94        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        61.41        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.33        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-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 
       26.04        27.02        16.01        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-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.08        10.06        12.03        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       11.51        20.42        18.25        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       49.91        12.59       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 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-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.31        29.59        13.25         0.53        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       28.21        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       55.04        51.75        39.42        35.93        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YX 
       52.80        19.33        19.33        15.65        13.05        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 
        8.42        31.30        70.03        39.48        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       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-3594 
        8.02         7.07        20.05        24.00         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
        0.99         1.02         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-4007 
       13.02        35.01        14.01         1.02        32.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
       17.03         0.99        20.98         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.72        26.43         1.81         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       78.12         7.17        10.98        15.02        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 TCGA-F5-6861 
       13.64        17.46         8.45        37.51         0.69         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          0.1                           0.0 
  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 
                        20.09                         19.00 
[1] "0.1 - 140.4 (20.1)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1"  
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   154  69
  DEL PEAK 11(4Q35.1) WILD-TYPE 288  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    154   69
  DEL PEAK 11(4Q35.1) WILD-TYPE  288   93
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON                          154                           288
  RECTUM                          69                            93
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q35.1) MUTATED        31        0        9        61         1
  DEL PEAK 11(4Q35.1) WILD-TYPE      73        1       27       110         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q35.1) MUTATED           1         9          8         33
  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           30       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                             31                            73
  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                          33                            46
  STAGE IIIC                          30                            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  34 160  26
  DEL PEAK 11(4Q35.1) WILD-TYPE  13  73 253  40
D38V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                           7                            13
  T2                          34                            73
  T3                         160                           253
  T4                          26                            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  64  57
  DEL PEAK 11(4Q35.1) WILD-TYPE 236  85  57
D38V6, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                         106                           236
  N1                          64                            85
  N2                          57                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   160  40
  DEL PEAK 11(4Q35.1) WILD-TYPE 288  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    160   40
  DEL PEAK 11(4Q35.1) WILD-TYPE  288   46
   clus
vv  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  0                         160                           288
  1                          40                            46
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   107 120
  DEL PEAK 11(4Q35.1) WILD-TYPE 179 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    107  120
  DEL PEAK 11(4Q35.1) WILD-TYPE  179  202
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                         107                           179
  MALE                           120                           202
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                    138
  DEL PEAK 11(4Q35.1) WILD-TYPE                  243
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              16
  DEL PEAK 11(4Q35.1) WILD-TYPE                            44
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                      65
  DEL PEAK 11(4Q35.1) WILD-TYPE                    81
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                3
  DEL PEAK 11(4Q35.1) WILD-TYPE                             10
D38V9, multiclass
                                clus
vv                               DEL PEAK 11(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                   138
  COLON MUCINOUS ADENOCARCINOMA                           16
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     243
  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     8 219
  DEL PEAK 11(4Q35.1) WILD-TYPE   1 380
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      8  219
  DEL PEAK 11(4Q35.1) WILD-TYPE    1  380
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                            8                             1
  YES                         219                           380
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q35.1) MUTATED   163   1  15   9
  DEL PEAK 11(4Q35.1) WILD-TYPE 276   4  21  20
D38V11, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         163                           276
  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                          27   109
  DEL PEAK 11(4Q35.1) WILD-TYPE                        33   183
D38V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 11(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   33
  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   112  36
  DEL PEAK 12(5Q12.1) WILD-TYPE 356  79
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          148                           435 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           36                            79 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.76        43.43        42.90        13.94        16.57 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 
       37.02        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        10.06        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        10.98        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        22.42        27.42         0.20 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4684 
       16.31         0.20        17.26        19.33         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 
       62.79        29.56         5.23         1.94         3.29         1.35 
TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       49.08        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 
        5.03        15.02        14.04        29.03        13.02        17.75 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB 
       17.85         7.53        10.13        12.43         9.04        44.32 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 
      131.51         6.12         8.61         1.55        33.67         8.35 
TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U 
       82.39        45.11        36.00        91.79        18.18        10.98 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       12.79        42.77         8.42         9.70        30.28        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 
       17.23        43.04        37.74        10.39        15.39        10.39 
TCGA-AF-A56K TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 
       86.63        29.98         1.02        32.98        19.99        17.03 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y 
        1.02        48.03        28.04        36.03        17.03        23.01 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 
       70.03        64.01         1.94        38.96        41.00        10.19 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        6.05         7.17        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98        13.05       126.44        57.24       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       20.55        16.41        13.64        11.97         8.45        37.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6641 
       28.57        32.19        18.28        26.43 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 
       11.47         4.80        11.47        46.65        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 
       44.91        35.11        45.60        37.05        37.25        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 
       32.71        29.16        22.52        24.13         8.38        20.61 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         7.04         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       29.00         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
        0.92        47.05        15.02        11.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       32.05        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       24.00        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        38.04         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72         5.79        10.88        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        18.84        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       23.05        20.02        37.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       12.00        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58        12.39        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38         7.50       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        35.87        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        35.41        19.43       107.67        28.21        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       51.75        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80        19.33        19.33         9.93        15.65        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       12.00        29.46        32.98        31.30        70.03        39.48 
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        16.83        20.02 
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        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        12.00        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       49.97        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        78.12        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       12.00        30.05        12.95        10.06         5.29        41.36 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6571 
        8.61        11.51        10.78        17.46         9.96        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         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 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       22.225                        18.250 
[1] "0.2 - 131.5 (22.2)" "0.0 - 140.4 (18.2)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   103  53
  DEL PEAK 12(5Q12.1) WILD-TYPE 339 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    103   53
  DEL PEAK 12(5Q12.1) WILD-TYPE  339  109
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON                          103                           339
  RECTUM                          53                           109
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(5Q12.1) MUTATED        25        0        7        34         1
  DEL PEAK 12(5Q12.1) WILD-TYPE      79        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         61
                               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         35       42        14         1
D39V4, multiclass
            clus
vv           DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  STAGE I                             25                            79
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           34                           137
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           9                            12
  STAGE IIIB                          18                            61
  STAGE IIIC                          19                            35
  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  29 105  17
  DEL PEAK 12(5Q12.1) WILD-TYPE  15  78 308  49
D39V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  T1                           5                            15
  T2                          29                            78
  T3                         105                           308
  T4                          17                            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 12(5Q12.1) MUTATED    74  44  38
  DEL PEAK 12(5Q12.1) WILD-TYPE 268 105  76
D39V6, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  N0                          74                           268
  N1                          44                           105
  N2                          38                            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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   102  31
  DEL PEAK 12(5Q12.1) WILD-TYPE 346  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    102   31
  DEL PEAK 12(5Q12.1) WILD-TYPE  346   55
   clus
vv  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  0                         102                           346
  1                          31                            55
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    71  85
  DEL PEAK 12(5Q12.1) WILD-TYPE 215 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     71   85
  DEL PEAK 12(5Q12.1) WILD-TYPE  215  237
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  FEMALE                          71                           215
  MALE                            85                           237
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                     95
  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                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                      50
  DEL PEAK 12(5Q12.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                2
  DEL PEAK 12(5Q12.1) WILD-TYPE                             11
D39V9, multiclass
                                clus
vv                               DEL PEAK 12(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                    95
  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                             52
  RECTAL ADENOCARCINOMA                                     96
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     8 148
  DEL PEAK 12(5Q12.1) WILD-TYPE   1 451
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      8  148
  DEL PEAK 12(5Q12.1) WILD-TYPE    1  451
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                            8                             1
  YES                         148                           451
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED   107   2   9   5
  DEL PEAK 12(5Q12.1) WILD-TYPE 332   3  27  24
D39V11, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                         107                           332
  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                          19    80
  DEL PEAK 12(5Q12.1) WILD-TYPE                        41   212
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     80
                                  clus
vv                                 DEL PEAK 12(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   41
  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   131  43
  DEL PEAK 13(5Q21.2) WILD-TYPE 337  72
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          174                           409 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                           43                            72 
$`DEL PEAK 13(5Q21.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       43.76        43.76        13.94        16.57        37.02        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        56.25 
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        10.06 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       36.95        37.02        10.06        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 
       10.98        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 
       22.42        27.42         0.20         0.46        16.31         0.20 
TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       21.44        19.33         5.65        83.80        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 
       29.56         5.23         1.94         2.24         3.29         1.35 
TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       49.08        25.02        26.04         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.03         5.03        15.02        14.04        29.03        13.02 
TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 
       11.08        19.59        20.42        15.12        17.85        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 
       12.43         9.04        13.41        11.38        92.75       140.38 
TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28H 
       44.32         7.76         6.12        14.04        26.47       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 
       98.24         8.61        13.38         1.55        33.67         8.35 
TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U 
       82.39        45.11        36.00        91.79        18.18        10.98 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       12.79        42.77         8.42         9.70        30.28        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 
       17.23        43.04        37.74        10.39        15.39        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
       86.63        65.98        32.02        19.99         7.99        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-A01W 
       28.04        36.03        17.03         6.02        23.01        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CI-6620 
       64.01         1.94        38.96        41.00        10.19         6.05 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.99        13.97        15.02        36.00        10.98        13.05 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6513 
      126.44        57.24        51.48        20.55        18.28        16.34 
TCGA-EI-6881 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
       16.41        13.64         9.96        28.57         0.46        18.28 

$`DEL PEAK 13(5Q21.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 
       24.33        42.28        44.91        35.11        45.60        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.25        34.65        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       16.24        24.92        61.84         7.04         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-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07         0.00        34.03        29.00        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        13.94        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-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        37.05        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       15.95        38.99        14.93         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
        0.00        36.03        32.05        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00W 
       18.05        18.05        38.04         4.01         0.99        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O 
       26.01        37.02        39.06        51.98        39.98         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-6964 
        4.21        56.55         0.79         0.72         5.79        10.88 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       23.05        20.02        37.02        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        13.51        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25         1.32        43.27         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         7.53        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       135.65       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       35.97        60.79        95.18        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        35.87        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        35.41        19.43       107.67        28.21        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       51.75        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80        19.33        19.33         9.93        15.65        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       12.00        29.46        32.98        31.30        70.03        39.48 
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        16.83        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        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        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        26.43         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        78.12         7.17        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        32.19         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 
                          0.2                           0.0 
  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 
                        19.99                         19.00 
[1] "0.2 - 140.4 (20.0)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.3"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   129  55
  DEL PEAK 13(5Q21.2) WILD-TYPE 313 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    129   55
  DEL PEAK 13(5Q21.2) WILD-TYPE  313  107
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON                          129                           313
  RECTUM                          55                           107
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q21.2) MUTATED        26        0        8        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         52
                               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         31       38        13         1
D40V4, multiclass
            clus
vv           DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  STAGE I                             26                            78
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           40                           131
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                          10                            11
  STAGE IIIB                          27                            52
  STAGE IIIC                          23                            31
  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  32 127  21
  DEL PEAK 13(5Q21.2) WILD-TYPE  16  75 286  45
D40V5, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            75
  T3                         127                           286
  T4                          21                            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 13(5Q21.2) MUTATED    83  56  45
  DEL PEAK 13(5Q21.2) WILD-TYPE 259  93  69
D40V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  N0                          83                           259
  N1                          56                            93
  N2                          45                            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"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   124  36
  DEL PEAK 13(5Q21.2) WILD-TYPE 324  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    124   36
  DEL PEAK 13(5Q21.2) WILD-TYPE  324   50
   clus
vv  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  0                         124                           324
  1                          36                            50
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED    86  98
  DEL PEAK 13(5Q21.2) WILD-TYPE 200 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED     86   98
  DEL PEAK 13(5Q21.2) WILD-TYPE  200  224
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  FEMALE                          86                           200
  MALE                            98                           224
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                    116
  DEL PEAK 13(5Q21.2) WILD-TYPE                  265
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                              13
  DEL PEAK 13(5Q21.2) WILD-TYPE                            47
                               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                                   116
  COLON MUCINOUS ADENOCARCINOMA                           13
  RECTAL ADENOCARCINOMA                                   53
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  COLON MUCINOUS ADENOCARCINOMA                             47
  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     8 176
  DEL PEAK 13(5Q21.2) WILD-TYPE   1 423
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED      8  176
  DEL PEAK 13(5Q21.2) WILD-TYPE    1  423
     clus
vv    DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  NO                            8                             1
  YES                         176                           423
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.2) MUTATED   124   2  13   7
  DEL PEAK 13(5Q21.2) WILD-TYPE 315   3  23  22
D40V11, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  R0                         124                           315
  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                          19    91
  DEL PEAK 13(5Q21.2) WILD-TYPE                        41   201
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK 13(5Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   41
  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   130  44
  DEL PEAK 14(5Q22.2) WILD-TYPE 338  71
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          174                           409 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           44                            71 
$`DEL PEAK 14(5Q22.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       43.76        43.76        13.94        16.57        37.02        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        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-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        10.98        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        22.42        27.42        10.88 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 
        0.20        16.31         0.20        21.44        19.33         5.65 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79         6.77        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6751 
        1.94         2.14         3.29         1.35        49.08       124.27 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 
       25.02        26.04         8.02        13.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 
       15.02        14.04        29.03        13.02        11.08        19.59 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.12        17.85        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 
       11.38        92.75       140.38        44.32         7.76         6.12 
TCGA-DM-A28A TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       26.47        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 
        1.55        33.67         8.35        82.39        45.11        36.00 
TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 
       91.79        18.18        10.98        12.79        42.77         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 
        9.70        30.28        24.13        17.23        43.04        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 
       10.39        15.39        10.39        86.63        65.98        32.02 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 
       19.99        29.98         1.02        32.98        19.99        17.03 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00C 
        1.02        48.03        28.04        36.03        17.03         6.02 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       23.01        12.00        70.03        64.01         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 
       41.00         1.81        10.19         6.05         7.17        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        10.98        13.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       41.36        57.24        51.48        20.55        19.96        18.28 
TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
       16.34        16.41         9.96        28.57         0.46        18.28 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 
       24.33        42.28        44.91        35.11        45.60        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.25        34.65        32.45        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        56.25         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        3.02        37.05        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07         0.00        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       29.00         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        13.94        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.05        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3715 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-3837 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        14.93         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        39.98         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.72         5.79        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       27.09         0.95        15.75        17.82        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        61.41        49.41        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19         2.24         3.06         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-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5341 
        2.01        23.05        20.02        37.02        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        7.53        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28M 
      139.17        14.04        81.37       119.93        35.97        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        46.75        47.15        52.80        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        13.05        12.00        29.46        32.98 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       31.30        70.03        39.48        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        16.83        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        36.03        20.05        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        26.43 
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        78.12 
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        32.19         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 
                          0.2                           0.0 
  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 
                        19.46                         19.00 
[1] "0.2 - 140.4 (19.5)" "0.0 - 139.2 (19.0)"
[1] "hr=" "1.3"
D41V2, continuous
D41V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   127  59
  DEL PEAK 14(5Q22.2) WILD-TYPE 315 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    127   59
  DEL PEAK 14(5Q22.2) WILD-TYPE  315  103
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON                          127                           315
  RECTUM                          59                           103
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q22.2) MUTATED        27        0        9        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         53
                               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         32       38        14         1
D41V4, multiclass
            clus
vv           DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  STAGE I                             27                            77
  STAGE IA                             0                             1
  STAGE II                             9                            27
  STAGE IIA                           44                           127
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           9                            12
  STAGE IIIB                          26                            53
  STAGE IIIC                          22                            32
  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  32 130  20
  DEL PEAK 14(5Q22.2) WILD-TYPE  16  75 283  46
D41V5, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            75
  T3                         130                           283
  T4                          20                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 14(5Q22.2) MUTATED    90  53  43
  DEL PEAK 14(5Q22.2) WILD-TYPE 252  96  71
D41V6, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          90                           252
  N1                          53                            96
  N2                          43                            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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   124  35
  DEL PEAK 14(5Q22.2) WILD-TYPE 324  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    124   35
  DEL PEAK 14(5Q22.2) WILD-TYPE  324   51
   clus
vv  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  0                         124                           324
  1                          35                            51
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    83 103
  DEL PEAK 14(5Q22.2) WILD-TYPE 203 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     83  103
  DEL PEAK 14(5Q22.2) WILD-TYPE  203  219
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          83                           203
  MALE                           103                           219
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                    115
  DEL PEAK 14(5Q22.2) WILD-TYPE                  266
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                              12
  DEL PEAK 14(5Q22.2) WILD-TYPE                            48
                               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                                   115
  COLON MUCINOUS ADENOCARCINOMA                           12
  RECTAL ADENOCARCINOMA                                   56
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     266
  COLON MUCINOUS ADENOCARCINOMA                             48
  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     8 178
  DEL PEAK 14(5Q22.2) WILD-TYPE   1 421
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      8  178
  DEL PEAK 14(5Q22.2) WILD-TYPE    1  421
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                            8                             1
  YES                         178                           421
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q22.2) MUTATED   121   2  15   8
  DEL PEAK 14(5Q22.2) WILD-TYPE 318   3  21  21
D41V11, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                         121                           318
  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                          18    93
  DEL PEAK 14(5Q22.2) WILD-TYPE                        42   199
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK 14(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  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 414  98
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           71                           512 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           17                            98 
$`DEL PEAK 15(6P25.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       43.76        16.57        37.02        25.18        24.16        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
       36.00        19.04        38.99        36.95        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 
       29.98        18.05        12.99        24.00         2.01        13.94 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O 
       30.02        18.05        27.02        38.07        26.01         0.92 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
        0.72         5.79        10.88        16.44         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
        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        45.40        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        37.25        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-A6-6650 TCGA-A6-6651 
       22.52        24.13         8.38        25.08        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        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        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 
       63.98         6.97         1.02        13.02        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-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-3562 
       17.95        29.95        23.01        20.98        19.99        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.05        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-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
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        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
        0.00        36.03        32.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       24.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        38.04         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       51.98         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21        56.55         0.79        22.42        27.42         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        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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        49.08        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        25.02        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        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        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 
       13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30         9.70        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       39.48        43.04        37.74        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03         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-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        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-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-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-6619 TCGA-CI-6620 
        0.69         0.72        26.43         1.81         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        78.12         7.17 
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-DY-A0XA 
       36.00        10.98        30.05        12.95        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        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-6884 
       17.69        16.34        16.31        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.72                          0.00 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       117.07                        140.38 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                        18.05                         19.33 
[1] "0.7 - 117.1 (18.1)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    54  21
  DEL PEAK 15(6P25.3) WILD-TYPE 388 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     54   21
  DEL PEAK 15(6P25.3) WILD-TYPE  388  141
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  COLON                           54                           388
  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      95        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         73
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(6P25.3) MUTATED            7        7         5         0
  DEL PEAK 15(6P25.3) WILD-TYPE         47       54        22         2
D42V4, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              9                            95
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           28                           143
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            4                            22
  STAGE IIIA                           1                            20
  STAGE IIIB                           6                            73
  STAGE IIIC                           7                            47
  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  98 356  56
D42V5, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T1                           2                            18
  T2                           9                            98
  T3                          57                           356
  T4                          10                            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 15(6P25.3) MUTATED    47  15  16
  DEL PEAK 15(6P25.3) WILD-TYPE 295 134  98
D42V6, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          47                           295
  N1                          15                           134
  N2                          16                            98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    55  11
  DEL PEAK 15(6P25.3) WILD-TYPE 393  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     55   11
  DEL PEAK 15(6P25.3) WILD-TYPE  393   75
   clus
vv  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  0                          55                           393
  1                          11                            75
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    29  49
  DEL PEAK 15(6P25.3) WILD-TYPE 257 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     29   49
  DEL PEAK 15(6P25.3) WILD-TYPE  257  273
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          29                           257
  MALE                            49                           273
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                     49
  DEL PEAK 15(6P25.3) WILD-TYPE                  332
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                               5
  DEL PEAK 15(6P25.3) WILD-TYPE                            55
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                      18
  DEL PEAK 15(6P25.3) WILD-TYPE                   128
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                                3
  DEL PEAK 15(6P25.3) WILD-TYPE                             10
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                                     332
  COLON MUCINOUS ADENOCARCINOMA                             55
  RECTAL ADENOCARCINOMA                                    128
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     2  76
  DEL PEAK 15(6P25.3) WILD-TYPE   7 523
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      2   76
  DEL PEAK 15(6P25.3) WILD-TYPE    7  523
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                            2                             7
  YES                          76                           523
[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 384   5  33  23
D42V11, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          55                           384
  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                        59   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                                   59
  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    62  23
  DEL PEAK 16(6Q26) WILD-TYPE 406  92
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         85                         498 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         23                          92 
$`DEL PEAK 16(6Q26) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6649 
       43.76        42.28        45.60        32.45        22.52        24.16 
TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       20.28         5.03        13.02        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3837 
       11.01        37.05        36.00        85.05        19.04        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        36.03        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        2.01        18.05        17.03        10.98        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         5.79        16.44         0.46        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 
        0.20        18.84         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 
       45.40        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         9.93        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       42.90        24.33        44.91        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-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-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-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-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.05         6.97        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        19.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00         2.01        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72        22.42        27.42        10.88         0.20 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       17.82        17.26        17.85        19.33        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        49.08        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        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        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        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       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        13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30         9.70        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       39.48        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 
       10.39        86.63        65.98        11.84        36.03         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 
        7.07        36.03        20.05         1.02        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-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-3999 TCGA-AG-4001 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        36.03        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
        0.99        20.98         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.04         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.81        10.19         6.05         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        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        10.98 
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-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        28.57         0.39        32.19         0.66 
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 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                        0.2                         0.0 
  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 
                      17.03                       19.81 
[1] "0.2 - 131.5 (17.0)" "0.0 - 140.4 (19.8)"
[1] "hr=" "1.7"
D43V2, continuous
D43V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    61  28
  DEL PEAK 16(6Q26) WILD-TYPE 381 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     61   28
  DEL PEAK 16(6Q26) WILD-TYPE  381  134
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  COLON                         61                         381
  RECTUM                        28                         134
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6Q26) MUTATED        13        0        8        20         1
  DEL PEAK 16(6Q26) WILD-TYPE      91        1       28       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         69
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6Q26) MUTATED           14       12         4         1
  DEL PEAK 16(6Q26) WILD-TYPE         40       49        23         1
D43V4, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                           13                          91
  STAGE IA                           0                           1
  STAGE II                           8                          28
  STAGE IIA                         20                         151
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          4                          22
  STAGE IIIA                         1                          20
  STAGE IIIB                        10                          69
  STAGE IIIC                        14                          40
  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  97 349  54
D43V5, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T1                         5                          15
  T2                        10                          97
  T3                        64                         349
  T4                        12                          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 16(6Q26) MUTATED    42  18  30
  DEL PEAK 16(6Q26) WILD-TYPE 300 131  84
D43V6, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                        42                         300
  N1                        18                         131
  N2                        30                          84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    59  18
  DEL PEAK 16(6Q26) WILD-TYPE 389  68
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     59   18
  DEL PEAK 16(6Q26) WILD-TYPE  389   68
   clus
vv  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  0                        59                         389
  1                        18                          68
[1] 2 2
[1] FALSE
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    37  54
  DEL PEAK 16(6Q26) WILD-TYPE 249 268
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     37   54
  DEL PEAK 16(6Q26) WILD-TYPE  249  268
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        37                         249
  MALE                          54                         268
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                     53
  DEL PEAK 16(6Q26) WILD-TYPE                  328
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                               8
  DEL PEAK 16(6Q26) WILD-TYPE                            52
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                      22
  DEL PEAK 16(6Q26) WILD-TYPE                   124
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                6
  DEL PEAK 16(6Q26) WILD-TYPE                              7
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                                   328
  COLON MUCINOUS ADENOCARCINOMA                           52
  RECTAL ADENOCARCINOMA                                  124
  RECTAL MUCINOUS ADENOCARCINOMA                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     2  89
  DEL PEAK 16(6Q26) WILD-TYPE   7 510
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      2   89
  DEL PEAK 16(6Q26) WILD-TYPE    7  510
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                          2                           7
  YES                        89                         510
[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 378   4  28  22
D43V11, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                        61                         378
  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                        55   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                                 55
  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 456 113
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           14                           569 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            2                           113 
$`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        38.04        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.43        42.90        24.33        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       36.53        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.18        24.16        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        5.79        22.42        27.42        10.88         0.20        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84        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        49.08        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        25.02 
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        45.40 
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        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 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        13.25 
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        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       12.79        13.05        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
        8.42        31.30         9.70        30.28        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        19.10        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        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-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-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         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        78.12         7.17        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 
       10.98        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-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         5.03                          0.00 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        38.04                        140.38 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                       18.195                        19.070 
[1] "5.0 - 38.0 (18.2)"  "0.0 - 140.4 (19.1)"
[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 430 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     12    4
  DEL PEAK 17(7Q31.1) WILD-TYPE  430  158
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON                           12                           430
  RECTUM                           4                           158
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(7Q31.1) MUTATED         3        0        0         7         0
  DEL PEAK 17(7Q31.1) WILD-TYPE     101        1       36       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         78
                               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         52       61        26         2
D44V4, multiclass
            clus
vv           DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  STAGE I                              3                           101
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                            7                           164
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            1                            25
  STAGE IIIA                           1                            20
  STAGE IIIB                           1                            78
  STAGE IIIC                           2                            52
  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  20 103 401  66
D44V5, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           103
  T3                          12                           401
  T4                           0                            66
[1] 4 2
[1] TRUE
[1] "dimension 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 332 146 111
D44V6, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                          10                           332
  N1                           3                           146
  N2                           3                           111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    15   1
  DEL PEAK 17(7Q31.1) WILD-TYPE 433  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     15    1
  DEL PEAK 17(7Q31.1) WILD-TYPE  433   85
   clus
vv  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  0                          15                           433
  1                           1                            85
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     9   7
  DEL PEAK 17(7Q31.1) WILD-TYPE 277 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      9    7
  DEL PEAK 17(7Q31.1) WILD-TYPE  277  315
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           9                           277
  MALE                             7                           315
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                     11
  DEL PEAK 17(7Q31.1) WILD-TYPE                  370
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                               1
  DEL PEAK 17(7Q31.1) WILD-TYPE                            59
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                       3
  DEL PEAK 17(7Q31.1) WILD-TYPE                   143
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                                1
  DEL PEAK 17(7Q31.1) WILD-TYPE                             12
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                                     370
  COLON MUCINOUS ADENOCARCINOMA                             59
  RECTAL ADENOCARCINOMA                                    143
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     0  16
  DEL PEAK 17(7Q31.1) WILD-TYPE   9 583
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      0   16
  DEL PEAK 17(7Q31.1) WILD-TYPE    9  583
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  NO                            0                             9
  YES                          16                           583
[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 424   5  36  29
D44V11, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  R0                          15                           424
  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                        60   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                                   60
  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  57
  DEL PEAK 18(8P23.2) WILD-TYPE 249  58
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          276                           307 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           57                            58 
$`DEL PEAK 18(8P23.2) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        4.80        43.76        43.76        43.43        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       44.91        35.11        45.60        16.57        34.65        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 
       32.91        31.63        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        56.25         9.63         5.03         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3531 
       37.05         1.02        38.99        24.03         0.00        34.03 
TCGA-AA-3532 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-3556 TCGA-AA-3560 TCGA-AA-3562 
       21.01        13.02        24.00        23.01        19.99        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 
       78.08         6.05         2.01        14.01        47.01        15.02 
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-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       33.07        36.03         0.99        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-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K 
       19.00        34.03        17.03        15.02        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J 
        1.02        33.04        37.02         2.96        39.98         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         5.79        22.42         0.20 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       16.31        15.75         0.20        17.85        18.84        75.25 
TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 
        5.65        83.80        65.00        62.79        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6715 
        5.23        11.74         3.19         1.94         3.29         0.07 
TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
        1.35        15.62        49.08        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 
       22.98        30.08        16.01         5.03        17.03        14.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       21.99        13.02        15.02        13.05        11.08        10.06 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
       12.26        13.51        11.51        17.75         1.32        43.27 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       15.12        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       49.91        13.32       140.38       131.51         6.12        26.47 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 
       35.97        60.79       117.07        13.38        13.64         1.55 
TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       16.31         0.53         8.35        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        39.42        35.93        36.72        36.00        26.43 
TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB 
       35.80        91.79        10.98        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 
       12.00         8.42         9.70        30.28        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 
       15.39        20.02        10.39        65.98        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 
       24.00         1.02        46.03        34.03         2.01         6.05 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
        0.99        19.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 
        0.99         1.02        17.03        35.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        25.97        23.01        15.95         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 
        1.94        38.96        41.00         1.45         0.72        10.19 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        13.97        78.12        10.98        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        36.00        10.98        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 
        5.29       126.44        41.36        57.24       129.27         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        2.40        15.85        16.34        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        31.30        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69         0.76         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 
       11.47        11.47        46.65        42.90        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 
       37.25        37.02        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 
        7.04         3.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-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 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 
       17.03        10.06         0.00         0.00        32.05        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       24.00        20.98         2.01        21.99        50.99        13.05 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
        0.99        14.99        21.99        34.98        15.02        10.98 
TCGA-AA-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-A02H TCGA-AA-A02O TCGA-AA-A02R 
       26.01        39.06        51.98         2.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88        16.44         0.46         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        17.26 
TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5254 
       22.36        61.41        49.41         6.77       100.01         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 
       17.56       102.44        40.34        70.16        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 
       37.02        25.02        26.04         8.02        29.06        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       11.01        12.03        45.40        19.59        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 
       18.25        17.85         4.80        17.13        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
      119.70        92.75        12.59         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K 
        7.76       139.17        14.04        81.37       119.93        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18         8.61        11.11        13.45         6.18        35.87 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67        13.25        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
      107.67        28.21        82.39        67.30        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 
       51.75        45.11        22.09        26.04        13.78        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC 
       46.75        47.15        52.80        18.18        19.33        12.79 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
       13.05        42.77        29.46        32.98        31.30        70.03 
TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       24.13        14.50        16.83        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 
       12.00         8.02         7.07        20.05        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       15.95        19.99         1.02         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       13.02        14.01        48.03         0.99        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       37.02        36.03        49.97        61.97        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69        26.43         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
        9.37         7.17        15.02        12.00        30.05        12.95 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        17.69        16.31        16.41         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 
       17.46        37.51        32.19         0.53         1.12        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                            0                             0 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        18.56                         19.33 
[1] "0.0 - 140.4 (18.6)" "0.0 - 139.2 (19.3)"
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   186  98
  DEL PEAK 18(8P23.2) WILD-TYPE 256  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    186   98
  DEL PEAK 18(8P23.2) WILD-TYPE  256   64
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  COLON                          186                           256
  RECTUM                          98                            64
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(8P23.2) MUTATED        40        0       12        64         3
  DEL PEAK 18(8P23.2) WILD-TYPE      64        1       24       107         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(8P23.2) MUTATED           2        14         11         43
  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         21       17        13         1
D45V4, multiclass
            clus
vv           DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                             40                            64
  STAGE IA                             0                             1
  STAGE II                            12                            24
  STAGE IIA                           64                           107
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           14                            12
  STAGE IIIA                          11                            10
  STAGE IIIB                          43                            36
  STAGE IIIC                          33                            21
  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  48 201  33
  DEL PEAK 18(8P23.2) WILD-TYPE  16  59 212  33
D45V5, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T1                           4                            16
  T2                          48                            59
  T3                         201                           212
  T4                          33                            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   132  80  72
  DEL PEAK 18(8P23.2) WILD-TYPE 210  69  42
D45V6, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                         132                           210
  N1                          80                            69
  N2                          72                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   197  57
  DEL PEAK 18(8P23.2) WILD-TYPE 251  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    197   57
  DEL PEAK 18(8P23.2) WILD-TYPE  251   29
   clus
vv  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  0                         197                           251
  1                          57                            29
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   121 165
  DEL PEAK 18(8P23.2) WILD-TYPE 165 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    121  165
  DEL PEAK 18(8P23.2) WILD-TYPE  165  157
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                         121                           165
  MALE                           165                           157
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                    169
  DEL PEAK 18(8P23.2) WILD-TYPE                  212
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                              16
  DEL PEAK 18(8P23.2) WILD-TYPE                            44
                               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                                   169
  COLON MUCINOUS ADENOCARCINOMA                           16
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 18(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     212
  COLON MUCINOUS ADENOCARCINOMA                             44
  RECTAL ADENOCARCINOMA                                     57
  RECTAL MUCINOUS ADENOCARCINOMA                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     7 279
  DEL PEAK 18(8P23.2) WILD-TYPE   2 320
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      7  279
  DEL PEAK 18(8P23.2) WILD-TYPE    2  320
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                            7                             2
  YES                         279                           320
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED   198   2  25   9
  DEL PEAK 18(8P23.2) WILD-TYPE 241   3  11  20
D45V11, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                         198                           241
  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                          30   136
  DEL PEAK 18(8P23.2) WILD-TYPE                        30   156
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 30
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   30
  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   222  65
  DEL PEAK 19(8P22) WILD-TYPE 246  50
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        287                         296 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                         65                          50 
$`DEL PEAK 19(8P22) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        4.80        43.76        43.76        43.43        24.33        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       44.91        35.11        45.60        16.57        34.65        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 
       32.91        31.63        30.44        29.19        23.61        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       27.09        24.13        25.08        25.18        20.61        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3529 
        1.02        37.05         1.02        38.99        24.03         0.00 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       21.01        13.02        24.00        23.01        19.99        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 
       78.08         6.05        54.02         2.01        14.01        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3858 
       85.05        37.02        10.06        33.07        36.03        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 
       31.07        17.03        24.03        27.02        29.98         2.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
        2.01        34.03        16.08        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00U 
       27.02         7.96        19.00        34.03        38.04        17.03 
TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       15.02        12.00        31.00         1.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 
        2.96         5.03        41.00        40.96         4.21         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
       22.42         0.20         0.46        16.31        15.75         0.20 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 
       17.85        19.33        18.84        75.25         5.65        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       22.36        65.00        62.79        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       11.74         3.19         1.94         3.29         1.35       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       15.62        49.08        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 
       30.08        16.01         5.03        17.03        14.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       13.02        15.02        11.01        13.05        11.08        10.06 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       12.26        19.59        13.51        11.51        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        15.12        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
      130.65        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 
        6.12        26.47        35.97        60.79       117.07         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 
       13.38        11.11        13.64         1.55        16.31        13.25 
TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        0.53         8.35        23.51        74.56        65.85        44.68 
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-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       35.80        91.79        46.75        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2689 
       15.65        12.00         8.42         9.70        30.28        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       10.39        15.39        20.02        10.39        65.98        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
        6.05         0.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 
        0.99         1.02        17.03        35.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 
        1.94        38.96        41.00         1.45         0.72        10.19 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        13.97        78.12        10.98        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        36.00        10.98        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 
        5.29       126.44        41.36        57.24       129.27         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        2.40        15.85        16.34        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        31.30        28.57         0.39 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         0.76         0.46        18.28        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 
       11.47        11.47        46.65        42.90        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 
       37.25        37.02        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         7.04 
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        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        36.95        14.93         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
        0.00        32.05         0.99        53.00        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 
        2.01        21.99        50.99        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-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        10.98        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-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37        56.55         0.79         0.72        27.42 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       10.88        16.44         0.92        14.50        27.09         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       21.44        17.82        17.26        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       32.94         5.13        61.41        49.41         6.77       100.01 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
        0.33         0.10        17.56        40.34        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         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-5341 
       20.02        37.02        25.02        26.04         8.02        29.06 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       16.04        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       11.01        12.03        45.40        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 
       17.85         4.80        17.13        16.14        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        12.59         7.50       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6569 
       14.04        81.37       119.93        98.24        95.18        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
        6.18        35.87        29.59        16.24        33.67        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 
       19.43       107.67        28.21        82.39        67.30        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 
       55.04        51.75        45.11        22.09        13.78        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 
       47.15        52.80        18.18        19.33        12.79        13.05 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       42.77        29.46        32.98        31.30        70.03        24.13 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        86.63        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
        8.02         7.07        20.05        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99        19.99         1.02         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       13.02        14.01        48.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
        6.02        36.03        49.97        61.97        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69        26.43         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
        9.37         7.17        15.02        12.00        30.05        12.95 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        17.69        16.31        16.41         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       17.46        37.51        32.19         0.66         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                          0                           0 
  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 
                      19.00                       19.07 
[1] "0.0 - 140.4 (19.0)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   199  98
  DEL PEAK 19(8P22) WILD-TYPE 243  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    199   98
  DEL PEAK 19(8P22) WILD-TYPE  243   64
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  COLON                        199                         243
  RECTUM                        98                          64
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P22) MUTATED        40        0       13        66         3
  DEL PEAK 19(8P22) WILD-TYPE      64        1       23       105         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P22) MUTATED           2        14         13         45
  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         18       17        10         1
D46V4, multiclass
            clus
vv           DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  STAGE I                           40                          64
  STAGE IA                           0                           1
  STAGE II                          13                          23
  STAGE IIA                         66                         105
  STAGE IIB                          3                           7
  STAGE IIC                          2                           1
  STAGE III                         14                          12
  STAGE IIIA                        13                           8
  STAGE IIIB                        45                          34
  STAGE IIIC                        36                          18
  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  48 211  36
  DEL PEAK 19(8P22) WILD-TYPE  16  59 202  30
D46V5, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  T1                         4                          16
  T2                        48                          59
  T3                       211                         202
  T4                        36                          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   136  83  78
  DEL PEAK 19(8P22) WILD-TYPE 206  66  36
D46V6, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  N0                       136                         206
  N1                        83                          66
  N2                        78                          36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   206  60
  DEL PEAK 19(8P22) WILD-TYPE 242  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    206   60
  DEL PEAK 19(8P22) WILD-TYPE  242   26
   clus
vv  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  0                       206                         242
  1                        60                          26
[1] 2 2
[1] FALSE
D46V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   131 168
  DEL PEAK 19(8P22) WILD-TYPE 155 154
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    131  168
  DEL PEAK 19(8P22) WILD-TYPE  155  154
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  FEMALE                       131                         155
  MALE                         168                         154
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                    181
  DEL PEAK 19(8P22) WILD-TYPE                  200
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                              17
  DEL PEAK 19(8P22) WILD-TYPE                            43
                             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                                 181
  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                           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"
D46V10, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED     7 292
  DEL PEAK 19(8P22) WILD-TYPE   2 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED      7  292
  DEL PEAK 19(8P22) WILD-TYPE    2  307
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  NO                          7                           2
  YES                       292                         307
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(8P22) MUTATED   211   2  25   8
  DEL PEAK 19(8P22) WILD-TYPE 228   3  11  21
D46V11, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  R0                       211                         228
  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                          31   147
  DEL PEAK 19(8P22) WILD-TYPE                        29   145
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 19(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               31
  WHITE                                                  147
                                  clus
vv                                 DEL PEAK 19(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      9
  BLACK OR AFRICAN AMERICAN                                 29
  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 433 104
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           46                           537 
  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                           11                           104 
$`DEL PEAK 20(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 
       24.33        42.28        44.91        16.57        36.53        20.61 
TCGA-A6-6654 TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-3681 
       23.87        38.99        34.03        14.01         2.01         5.98 
TCGA-AA-3842 TCGA-AA-3989 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02F TCGA-AY-6196 
       37.02         7.96        10.98        31.00        39.98         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 
       17.85        18.84        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 
       39.48        13.55        12.72        36.03        29.98        17.03 
TCGA-AG-3909 TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6156 
       19.99        12.00        38.96        41.00        13.97        15.02 
TCGA-DY-A1DG TCGA-EI-6513 TCGA-F5-6810 TCGA-F5-6813 
       51.48        16.34         0.39         0.69 

$`DEL PEAK 20(8Q11.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       43.43        42.90        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
       29.00        29.00        26.01        12.99         0.99        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-3685 TCGA-AA-3688 
       47.05        47.01        15.02        11.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
       22.42        27.42        10.88         0.20        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.26        19.33        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        49.08        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        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        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        45.40        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        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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 
       13.25         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        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        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        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       31.30         9.70        30.28        70.03        24.13        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-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-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-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-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-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-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00        10.98        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-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-6514 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        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        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE 
                          0.2                           0.0 
  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 
                       19.415                        19.070 
[1] "0.2 - 131.5 (19.4)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.2"
D47V2, continuous
D47V3, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    30  16
  DEL PEAK 20(8Q11.1) WILD-TYPE 412 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     30   16
  DEL PEAK 20(8Q11.1) WILD-TYPE  412  146
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  COLON                           30                           412
  RECTUM                          16                           146
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8Q11.1) MUTATED         4        0        0        13         1
  DEL PEAK 20(8Q11.1) WILD-TYPE     100        1       36       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         72
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8Q11.1) MUTATED            7        6         4         1
  DEL PEAK 20(8Q11.1) WILD-TYPE         47       55        23         1
D47V4, multiclass
            clus
vv           DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  STAGE I                              4                           100
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                           13                           158
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           2                            19
  STAGE IIIB                           7                            72
  STAGE IIIC                           7                            47
  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  20 100 378  61
D47V5, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  T1                           0                            20
  T2                           7                           100
  T3                          35                           378
  T4                           5                            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 20(8Q11.1) MUTATED    19  16  12
  DEL PEAK 20(8Q11.1) WILD-TYPE 323 133 102
D47V6, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  N0                          19                           323
  N1                          16                           133
  N2                          12                           102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    32  11
  DEL PEAK 20(8Q11.1) WILD-TYPE 416  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     32   11
  DEL PEAK 20(8Q11.1) WILD-TYPE  416   75
   clus
vv  DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  0                          32                           416
  1                          11                            75
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED    18  29
  DEL PEAK 20(8Q11.1) WILD-TYPE 268 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED     18   29
  DEL PEAK 20(8Q11.1) WILD-TYPE  268  293
        clus
vv       DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  FEMALE                          18                           268
  MALE                            29                           293
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                     26
  DEL PEAK 20(8Q11.1) WILD-TYPE                  355
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                               4
  DEL PEAK 20(8Q11.1) WILD-TYPE                            56
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                      15
  DEL PEAK 20(8Q11.1) WILD-TYPE                   131
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8Q11.1) MUTATED                                1
  DEL PEAK 20(8Q11.1) WILD-TYPE                             12
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                                     355
  COLON MUCINOUS ADENOCARCINOMA                             56
  RECTAL ADENOCARCINOMA                                    131
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                               cls
clus                              0   1
  DEL PEAK 20(8Q11.1) MUTATED     1  46
  DEL PEAK 20(8Q11.1) WILD-TYPE   8 553
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(8Q11.1) MUTATED      1   46
  DEL PEAK 20(8Q11.1) WILD-TYPE    8  553
     clus
vv    DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  NO                            1                             8
  YES                          46                           553
[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 401   5  32  29
D47V11, multiclass
    clus
vv   DEL PEAK 20(8Q11.1) MUTATED DEL PEAK 20(8Q11.1) WILD-TYPE
  R0                          38                           401
  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                        54   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                                   54
  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    61  17
  DEL PEAK 21(9P24.2) WILD-TYPE 407  98
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           78                           505 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                           17                            98 
$`DEL PEAK 21(9P24.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 
       43.76        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        43.27         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         9.93        24.13        13.55 
TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 
       65.98        20.05        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-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.76        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        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-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-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-3710 
       11.01         5.98        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       19.04        19.04        10.06        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       41.00        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         5.79        22.42        27.42        10.88 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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        49.08        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 
       25.02        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        45.40        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 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         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        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        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        18.18        10.98        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30         9.70        30.28        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        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        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        7.07        36.03        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        32.98         0.99         0.99 
TCGA-AG-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-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-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-6623 TCGA-CL-5917 
       26.43         1.81         6.05         6.97         9.37        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        10.98        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        10.98        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
        5.29       126.44        41.36       129.27        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         0.66         0.69 
TCGA-F5-6861 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 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE 
                       15.485                        19.330 
[1] "0.2 - 85.0 (15.5)"  "0.0 - 140.4 (19.3)"
[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 387 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     55   26
  DEL PEAK 21(9P24.2) WILD-TYPE  387  136
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  COLON                           55                           387
  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      91        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         67
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(9P24.2) MUTATED            9       12         4         1
  DEL PEAK 21(9P24.2) WILD-TYPE         45       49        23         1
D48V4, multiclass
            clus
vv           DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  STAGE I                             13                            91
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           18                           153
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            3                            23
  STAGE IIIA                           3                            18
  STAGE IIIB                          12                            67
  STAGE IIIC                           9                            45
  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  90 362  54
D48V5, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  T1                           2                            18
  T2                          17                            90
  T3                          51                           362
  T4                          12                            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 21(9P24.2) MUTATED    38  23  20
  DEL PEAK 21(9P24.2) WILD-TYPE 304 126  94
D48V6, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  N0                          38                           304
  N1                          23                           126
  N2                          20                            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"
D48V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    57  18
  DEL PEAK 21(9P24.2) WILD-TYPE 391  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     57   18
  DEL PEAK 21(9P24.2) WILD-TYPE  391   68
   clus
vv  DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  0                          57                           391
  1                          18                            68
[1] 2 2
[1] FALSE
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(9P24.2) MUTATED    30  52
  DEL PEAK 21(9P24.2) WILD-TYPE 256 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED     30   52
  DEL PEAK 21(9P24.2) WILD-TYPE  256  270
        clus
vv       DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  FEMALE                          30                           256
  MALE                            52                           270
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                     52
  DEL PEAK 21(9P24.2) WILD-TYPE                  329
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(9P24.2) MUTATED                               3
  DEL PEAK 21(9P24.2) WILD-TYPE                            57
                               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                                     329
  COLON MUCINOUS ADENOCARCINOMA                             57
  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   7 519
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(9P24.2) MUTATED      2   80
  DEL PEAK 21(9P24.2) WILD-TYPE    7  519
     clus
vv    DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  NO                            2                             7
  YES                          80                           519
[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 387   3  29  26
D48V11, multiclass
    clus
vv   DEL PEAK 21(9P24.2) MUTATED DEL PEAK 21(9P24.2) WILD-TYPE
  R0                          52                           387
  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                        54   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                                   54
  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    91  19
  DEL PEAK 22(10P15.3) WILD-TYPE 377  96
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           110                            473 
  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                            19                             96 
$`DEL PEAK 22(10P15.3) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 
       43.76        24.33        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3673 
        1.02         6.97        13.02        19.99        54.02        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       37.05        36.00        85.05        10.06        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       24.03         2.01        50.99        24.00         7.96        34.03 
TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       18.05        42.02        21.99        10.98        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4323 
       22.42        16.44         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        65.85        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        12.79        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 
       28.57        26.43 

$`DEL PEAK 22(10P15.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.06        27.09        24.13         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92        56.25         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        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-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 
       37.02        14.93         0.00        17.03         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-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-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-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-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         5.79        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       10.88         0.20         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       15.75        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 
       18.84        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        49.08        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        25.02        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        45.40        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        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 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        13.25         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 
       67.30        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        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        13.05        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       29.46        32.98         8.42        31.30         9.70        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       39.48        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       14.50        16.83        15.39        20.02        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       20.05        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        1.02        32.98         0.99         0.99        19.99        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-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-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-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-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.94        38.96        61.97        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        78.12         7.17        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.99        12.00        10.98        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        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-6883 TCGA-EI-6884 
       15.85        17.69        16.34         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        18.28        55.76        47.08 

  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE 
                           0.2                            0.0 
  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 
                         19.99                          19.07 
[1] "0.2 - 129.3 (20.0)" "0.0 - 140.4 (19.1)"
[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 365 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     77   34
  DEL PEAK 22(10P15.3) WILD-TYPE  365  128
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  COLON                            77                            365
  RECTUM                           34                            128
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(10P15.3) MUTATED        19        0        6        21         0
  DEL PEAK 22(10P15.3) WILD-TYPE      85        1       30       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         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(10P15.3) MUTATED           13       17         7         1
  DEL PEAK 22(10P15.3) WILD-TYPE         41       44        20         1
D49V4, multiclass
            clus
vv           DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            21                            150
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            7                             14
  STAGE IIIB                           15                             64
  STAGE IIIC                           13                             41
  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  84 339  53
D49V5, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  T1                            2                             18
  T2                           23                             84
  T3                           74                            339
  T4                           13                             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 22(10P15.3) MUTATED    51  32  29
  DEL PEAK 22(10P15.3) WILD-TYPE 291 117  85
D49V6, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  N0                           51                            291
  N1                           32                            117
  N2                           29                             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"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    77  24
  DEL PEAK 22(10P15.3) WILD-TYPE 371  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     77   24
  DEL PEAK 22(10P15.3) WILD-TYPE  371   62
   clus
vv  DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  0                           77                            371
  1                           24                             62
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED    51  61
  DEL PEAK 22(10P15.3) WILD-TYPE 235 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED     51   61
  DEL PEAK 22(10P15.3) WILD-TYPE  235  261
        clus
vv       DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  FEMALE                           51                            235
  MALE                             61                            261
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                     69
  DEL PEAK 22(10P15.3) WILD-TYPE                  312
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                               8
  DEL PEAK 22(10P15.3) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                      30
  DEL PEAK 22(10P15.3) WILD-TYPE                   116
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(10P15.3) MUTATED                                4
  DEL PEAK 22(10P15.3) WILD-TYPE                              9
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                                      312
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     116
  RECTAL MUCINOUS ADENOCARCINOMA                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                                cls
clus                               0   1
  DEL PEAK 22(10P15.3) MUTATED     5 107
  DEL PEAK 22(10P15.3) WILD-TYPE   4 492
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(10P15.3) MUTATED      5  107
  DEL PEAK 22(10P15.3) WILD-TYPE    4  492
     clus
vv    DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  NO                             5                              4
  YES                          107                            492
[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 356   5  30  23
D49V11, multiclass
    clus
vv   DEL PEAK 22(10P15.3) MUTATED DEL PEAK 22(10P15.3) WILD-TYPE
  R0                           83                            356
  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                        51   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                                    51
  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   104  26
  DEL PEAK 23(10Q21.1) WILD-TYPE 364  89
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           130                            453 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            26                             89 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4107 
       43.76        24.33        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        56.25         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        10.06        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        10.98         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        22.42        16.44        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
       16.31         0.20        18.84         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 
       43.27        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        12.79 
TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 
       13.05        30.28        24.13        13.55        12.72        16.83 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
       10.39        65.98        32.02        36.03        20.05        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        28.57         0.46        26.43 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        36.53        14.53        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        24.16        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        5.03         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       58.03        63.98         1.02        13.02         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-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-3688 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        19.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        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-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98         2.96         2.01         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-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.72         5.79        27.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.26        17.85        19.33        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 
       49.08        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        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        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        45.40        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 
        4.80        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        13.25 
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        67.30        65.85        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
        9.70        70.03        39.48        17.23        43.04        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       37.74        10.39        14.50        15.39        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3584 
       11.84        36.03        12.00         8.02         7.07        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-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        19.99        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 
        1.02        17.03         0.99        20.98        37.02        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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       10.98        51.98        49.97        38.96        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       10.19         6.05         6.05         9.37        78.12         7.17 
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-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        30.05        12.95         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-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-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       11.97         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           0.2                            0.0 
  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 
                         19.99                          19.07 
[1] "0.2 - 129.3 (20.0)" "0.0 - 140.4 (19.1)"
[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 348 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     94   40
  DEL PEAK 23(10Q21.1) WILD-TYPE  348  122
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON                            94                            348
  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      84        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         61
                                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         35       42        21         1
D50V4, multiclass
            clus
vv           DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              7                             29
  STAGE IIA                            31                            140
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            7                             14
  STAGE IIIB                           18                             61
  STAGE IIIC                           19                             35
  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  83 319  52
D50V5, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  T1                            3                             17
  T2                           24                             83
  T3                           94                            319
  T4                           14                             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 23(10Q21.1) MUTATED    66  36  33
  DEL PEAK 23(10Q21.1) WILD-TYPE 276 113  81
D50V6, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  N0                           66                            276
  N1                           36                            113
  N2                           33                             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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    97  25
  DEL PEAK 23(10Q21.1) WILD-TYPE 351  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     97   25
  DEL PEAK 23(10Q21.1) WILD-TYPE  351   61
   clus
vv  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  0                           97                            351
  1                           25                             61
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    62  73
  DEL PEAK 23(10Q21.1) WILD-TYPE 224 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     62   73
  DEL PEAK 23(10Q21.1) WILD-TYPE  224  249
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  FEMALE                           62                            224
  MALE                             73                            249
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                     87
  DEL PEAK 23(10Q21.1) WILD-TYPE                  294
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                               7
  DEL PEAK 23(10Q21.1) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                      34
  DEL PEAK 23(10Q21.1) WILD-TYPE                   112
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                                6
  DEL PEAK 23(10Q21.1) WILD-TYPE                              7
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                                      294
  COLON MUCINOUS ADENOCARCINOMA                              53
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED     5 130
  DEL PEAK 23(10Q21.1) WILD-TYPE   4 469
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED      5  130
  DEL PEAK 23(10Q21.1) WILD-TYPE    4  469
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                             5                              4
  YES                          130                            469
[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 344   3  24  22
D50V11, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           95                            344
  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                        46   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                                    46
  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  25
  DEL PEAK 24(10Q23.31) WILD-TYPE 343  90
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            150                             433 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             25                              90 
$`DEL PEAK 24(10Q23.31) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       43.76        24.33        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 
       10.98        33.04        26.01        39.98        41.00        22.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
       16.44         0.46        14.50        16.31        17.26        17.85 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
        5.65        65.00        62.79        29.56         3.19         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        43.27        17.85        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.13         9.04        13.41       130.65        13.32       140.38 
TCGA-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        12.79        13.05 
TCGA-QG-A5YW TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 
       29.46        30.28        24.13        39.48        13.55        12.72 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       10.39        65.98        32.02         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3887 TCGA-AG-3896 
       50.04         6.05        29.98         1.02        36.95         1.02 
TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 
       19.99        13.94        25.97        37.02        12.00        10.98 
TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       41.00        26.43        10.19         6.97         4.73        13.97 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF 
       13.97        36.00        13.05        10.06       129.27        24.13 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
        0.49         2.40        17.00        16.34        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       11.97        28.57         0.66         0.46        47.08        26.43 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.90        44.91        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        5.03         7.04         3.02        37.05         1.02        35.01 
TCGA-AA-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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05        36.03         8.05         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       14.01        21.01        24.00        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       19.99        13.94        61.02        78.08         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        37.02        14.93         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       27.42        10.88         0.20         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82        19.33        18.84 
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        49.08        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        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       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        45.40        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         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         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 
       13.25         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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        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        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.00        42.77        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
        9.70        70.03        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       10.39        14.50        16.83        15.39        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       20.05        24.00         2.01        12.03         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-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-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-A01W 
       15.95        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        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-6903 
       38.04         0.49         1.45         0.69         0.72         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.05         9.37        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       11.01        15.02        12.99        12.00        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
       32.19         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 
       55.76 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.26                            0.00 
  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 
                          18.66                           19.07 
[1] "0.3 - 140.4 (18.7)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.2"
D51V2, continuous
D51V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   106  51
  DEL PEAK 24(10Q23.31) WILD-TYPE 336 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    106   51
  DEL PEAK 24(10Q23.31) WILD-TYPE  336  111
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON                            106                             336
  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      83        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         59
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q23.31) MUTATED           18       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                              83
  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                              59
  STAGE IIIC                            18                              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  24 113  16
  DEL PEAK 24(10Q23.31) WILD-TYPE  17  83 300  50
D51V5, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  T1                             3                              17
  T2                            24                              83
  T3                           113                             300
  T4                            16                              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 24(10Q23.31) MUTATED    76  44  37
  DEL PEAK 24(10Q23.31) WILD-TYPE 266 105  77
D51V6, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  N0                            76                             266
  N1                            44                             105
  N2                            37                              77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   114  29
  DEL PEAK 24(10Q23.31) WILD-TYPE 334  57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    114   29
  DEL PEAK 24(10Q23.31) WILD-TYPE  334   57
   clus
vv  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  0                           114                             334
  1                            29                              57
[1] 2 2
[1] FALSE
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    75  83
  DEL PEAK 24(10Q23.31) WILD-TYPE 211 239
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     75   83
  DEL PEAK 24(10Q23.31) WILD-TYPE  211  239
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                            75                             211
  MALE                              83                             239
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                     96
  DEL PEAK 24(10Q23.31) WILD-TYPE                  285
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                               9
  DEL PEAK 24(10Q23.31) WILD-TYPE                            51
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                      42
  DEL PEAK 24(10Q23.31) WILD-TYPE                   104
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                                7
  DEL PEAK 24(10Q23.31) WILD-TYPE                              6
D51V9, multiclass
                                clus
vv                               DEL PEAK 24(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                      96
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                     42
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       285
  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     6 152
  DEL PEAK 24(10Q23.31) WILD-TYPE   3 447
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED      6  152
  DEL PEAK 24(10Q23.31) WILD-TYPE    3  447
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                              6                               3
  YES                           152                             447
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(10Q23.31) MUTATED   116   1  12   6
  DEL PEAK 24(10Q23.31) WILD-TYPE 323   4  24  23
D51V11, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                           116                             323
  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                          16    81
  DEL PEAK 24(10Q23.31) WILD-TYPE                        44   211
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                       81
                                  clus
vv                                 DEL PEAK 24(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     44
  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   114  32
  DEL PEAK 25(10Q25.2) WILD-TYPE 354  83
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           146                            437 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                            32                             83 
$`DEL PEAK 25(10Q25.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
       11.47        43.76        24.33        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        56.25         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        10.06         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        10.98        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        22.42         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 
       16.44        14.50        16.31        17.85         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        25.02         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        43.27        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        12.79 
TCGA-NH-A8F7 TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 
       13.05        30.28        24.13        39.48        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 
       26.43        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        28.57         0.66         0.46 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK 25(10Q25.2) WILD-TYPE`
TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        13.94        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 
       20.12        19.66        20.28        16.24        24.92         7.04 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99         0.99        14.01        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-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-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-3681 TCGA-AA-3688 TCGA-AA-3710 
       47.05        47.01        15.02         5.98        19.00        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        19.04        35.05        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       10.06         0.00         0.00        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        38.04         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        35.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        5.79        27.42        10.88         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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 
       49.08        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 
       45.40        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         4.80        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        13.25 
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        67.30        65.85        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 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.00        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
        9.70        70.03        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       10.39        14.50        16.83        15.39        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
        1.02        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        1.81         6.05         6.05         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00        15.02        10.98        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        37.51        31.30         0.39        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        18.28        55.76 

  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                         19.99                          19.07 
[1] "0.2 - 140.4 (20.0)" "0.0 - 139.2 (19.1)"
[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 336 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    106   47
  DEL PEAK 25(10Q25.2) WILD-TYPE  336  115
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON                           106                            336
  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      85        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         60
                                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         35       39        21         1
D52V4, multiclass
            clus
vv           DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            41                            130
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                            7                             14
  STAGE IIIB                           19                             60
  STAGE IIIC                           19                             35
  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  85 299  52
D52V5, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  T1                            3                             17
  T2                           22                             85
  T3                          114                            299
  T4                           14                             52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 25(10Q25.2) MUTATED    73  42  38
  DEL PEAK 25(10Q25.2) WILD-TYPE 269 107  76
D52V6, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  N0                           73                            269
  N1                           42                            107
  N2                           38                             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"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   112  28
  DEL PEAK 25(10Q25.2) WILD-TYPE 336  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    112   28
  DEL PEAK 25(10Q25.2) WILD-TYPE  336   58
   clus
vv  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  0                          112                            336
  1                           28                             58
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    73  81
  DEL PEAK 25(10Q25.2) WILD-TYPE 213 241
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     73   81
  DEL PEAK 25(10Q25.2) WILD-TYPE  213  241
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  FEMALE                           73                            213
  MALE                             81                            241
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                     97
  DEL PEAK 25(10Q25.2) WILD-TYPE                  284
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                               9
  DEL PEAK 25(10Q25.2) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                      39
  DEL PEAK 25(10Q25.2) WILD-TYPE                   107
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                                7
  DEL PEAK 25(10Q25.2) WILD-TYPE                              6
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                                      284
  COLON MUCINOUS ADENOCARCINOMA                              51
  RECTAL ADENOCARCINOMA                                     107
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED     6 148
  DEL PEAK 25(10Q25.2) WILD-TYPE   3 451
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED      6  148
  DEL PEAK 25(10Q25.2) WILD-TYPE    3  451
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  NO                             6                              3
  YES                          148                            451
[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 327   4  24  23
D52V11, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  R0                          112                            327
  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                        45   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                                    45
  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  21
  DEL PEAK 26(11Q22.3) WILD-TYPE 385  94
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           104                            479 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                            21                             94 
$`DEL PEAK 26(11Q22.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       43.76        45.60        16.57        36.53        32.45        30.44 
TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3511 
       22.52        24.16        21.76        23.87         5.03         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3558 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3680 
        9.07        37.05        20.98         6.05         2.01        11.01 
TCGA-AA-3692 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.00        32.05        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-A00F 
        2.01        34.03         2.01        21.99        50.99        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J 
       42.02        32.02        33.04         2.96        39.98        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 
        5.79        22.42        16.44        14.50         0.95         0.20 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 
       17.85        19.33         1.41         2.14         0.26         2.01 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6172 
       30.08         5.03        15.02        15.02        14.04        11.01 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6924 TCGA-DM-A1D0 
       11.01        45.40        20.19        17.85        14.30       130.65 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6461 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
       49.91         7.50        11.11        36.72        36.00        46.75 
TCGA-NH-A50T TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       18.18        12.79        30.28        43.04        13.55        19.10 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 
       14.50        15.39        10.39        32.02         7.07        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3896 
       34.03         2.01         6.05         0.99        32.98         1.02 
TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02X 
       13.94        12.00        70.03        64.01        10.98        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 
        0.49         0.69         0.72        10.19        13.97        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 
       10.98        30.05         5.29        24.13        20.91        17.00 
TCGA-EI-6881 TCGA-EI-7004 
       16.41         8.45 

$`DEL PEAK 26(11Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 
       42.90        24.33        42.28        44.91        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-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-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
       78.08         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00         2.01        33.01        26.01        24.00        20.98 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        39.06        51.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       22.03        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72        27.42        10.88 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
        0.20         0.46         0.92        27.09        16.31        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.26        18.84        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         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        49.08        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        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       16.01        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       14.04        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 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-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       17.75        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       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-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U 
       35.80        26.17        91.79        47.15        52.80        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30         9.70 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 
       70.03        24.13        39.48        17.23        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       10.39        16.83        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         8.02        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        1.02        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        1.02        31.00        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       61.97        38.04         1.45        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37         4.73        78.12         7.17 
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-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       36.00        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        19.96        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           0.2                            0.0 
  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 
                        16.785                         19.590 
[1] "0.2 - 130.7 (16.8)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1.3"
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    70  36
  DEL PEAK 26(11Q22.3) WILD-TYPE 372 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     70   36
  DEL PEAK 26(11Q22.3) WILD-TYPE  372  126
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON                            70                            372
  RECTUM                           36                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(11Q22.3) MUTATED        22        0        4        26         0
  DEL PEAK 26(11Q22.3) WILD-TYPE      82        1       32       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         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(11Q22.3) MUTATED           11       14         5         1
  DEL PEAK 26(11Q22.3) WILD-TYPE         43       47        22         1
D53V4, multiclass
            clus
vv           DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  STAGE I                              22                             82
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            26                            145
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                            3                             18
  STAGE IIIB                           15                             64
  STAGE IIIC                           11                             43
  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  19  72  15
  DEL PEAK 26(11Q22.3) WILD-TYPE  16  88 341  51
D53V5, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  T1                            4                             16
  T2                           19                             88
  T3                           72                            341
  T4                           15                             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 26(11Q22.3) MUTATED    53  32  24
  DEL PEAK 26(11Q22.3) WILD-TYPE 289 117  90
D53V6, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  N0                           53                            289
  N1                           32                            117
  N2                           24                             90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    76  18
  DEL PEAK 26(11Q22.3) WILD-TYPE 372  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     76   18
  DEL PEAK 26(11Q22.3) WILD-TYPE  372   68
   clus
vv  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  0                           76                            372
  1                           18                             68
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    54  56
  DEL PEAK 26(11Q22.3) WILD-TYPE 232 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     54   56
  DEL PEAK 26(11Q22.3) WILD-TYPE  232  266
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  FEMALE                           54                            232
  MALE                             56                            266
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                     62
  DEL PEAK 26(11Q22.3) WILD-TYPE                  319
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                               8
  DEL PEAK 26(11Q22.3) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                      29
  DEL PEAK 26(11Q22.3) WILD-TYPE                   117
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                                6
  DEL PEAK 26(11Q22.3) WILD-TYPE                              7
D53V9, multiclass
                                clus
vv                               DEL PEAK 26(11Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     62
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      319
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     117
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED     3 107
  DEL PEAK 26(11Q22.3) WILD-TYPE   6 492
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED      3  107
  DEL PEAK 26(11Q22.3) WILD-TYPE    6  492
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  NO                             3                              6
  YES                          107                            492
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(11Q22.3) MUTATED    78   0   9   4
  DEL PEAK 26(11Q22.3) WILD-TYPE 361   5  27  25
D53V11, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  R0                           78                            361
  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                           6    53
  DEL PEAK 26(11Q22.3) WILD-TYPE                        54   239
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 26(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    54
  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    64  23
  DEL PEAK 27(12P13.1) WILD-TYPE 404  92
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            87                            496 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            23                             92 
$`DEL PEAK 27(12P13.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 
        4.80        43.76        24.33        45.60        34.65        36.53 
TCGA-A6-5659 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 
       30.44        24.69        20.28        61.84         9.63        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 
       14.01        33.99        13.02        78.08         2.01        50.04 
TCGA-AA-3688 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       19.00        31.07        17.03        24.03         2.01        50.99 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       32.02        33.04         2.96         5.79        22.42        16.44 
TCGA-AZ-4684 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 
       65.00         2.14         0.07        49.08         8.02         5.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 
       14.04        29.03        15.02        11.01        11.08        10.06 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 
        1.32        15.12         7.53        11.38        13.32        12.59 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
       13.38        11.11        16.24        65.85        36.72        36.00 
TCGA-G4-6586 TCGA-NH-A50U TCGA-NH-A8F7 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2691 
       35.80        10.98        13.05         9.70        30.28        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       13.55        19.10        10.39        14.50        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3898 TCGA-AG-A00C 
       36.03        34.03        29.98         1.02        48.03         6.02 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AH-6544 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6158 
       70.03         1.94         0.49         6.05        13.97        10.98 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
       24.13        51.48        20.91        17.00        16.31        16.41 
TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6641 
       28.57         0.66        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 
       11.47        11.47        46.65        43.76        43.43        42.90 
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        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        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        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       19.07         0.00        19.07        34.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       12.99         0.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.72        27.42        10.88         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
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-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        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-5796 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        12.26        19.59        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        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 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-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 
       24.43        38.20       130.65        92.75        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       60.79       117.07        98.24        95.18         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         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        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 
       35.93        26.43        22.09        26.04        13.78        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        12.00        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       29.46        32.98         8.42        31.30        70.03        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 
       39.48        17.23        12.72        37.74        16.83        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        36.03        20.05        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        26.43         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        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        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        32.19         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                           0.00 
  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 
                         16.44                          19.33 
[1] "0.1 - 78.1 (16.4)"  "0.0 - 140.4 (19.3)"
[1] "hr=" "1.6"
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    59  29
  DEL PEAK 27(12P13.1) WILD-TYPE 383 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     59   29
  DEL PEAK 27(12P13.1) WILD-TYPE  383  133
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  COLON                            59                            383
  RECTUM                           29                            133
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.1) MUTATED        14        0        5        17         1
  DEL PEAK 27(12P13.1) WILD-TYPE      90        1       31       154         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.1) MUTATED           0         2          5         13
  DEL PEAK 27(12P13.1) WILD-TYPE         3        24         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         42       50        19         2
D54V4, multiclass
            clus
vv           DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  STAGE I                              14                             90
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            17                            154
  STAGE IIB                             1                              9
  STAGE IIC                             0                              3
  STAGE III                             2                             24
  STAGE IIIA                            5                             16
  STAGE IIIB                           13                             66
  STAGE IIIC                           12                             42
  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  14  65   8
  DEL PEAK 27(12P13.1) WILD-TYPE  16  93 348  58
D54V5, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  T1                            4                             16
  T2                           14                             93
  T3                           65                            348
  T4                            8                             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    41  32  18
  DEL PEAK 27(12P13.1) WILD-TYPE 301 117  96
D54V6, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  N0                           41                            301
  N1                           32                            117
  N2                           18                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    57  19
  DEL PEAK 27(12P13.1) WILD-TYPE 391  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     57   19
  DEL PEAK 27(12P13.1) WILD-TYPE  391   67
   clus
vv  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  0                           57                            391
  1                           19                             67
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    44  47
  DEL PEAK 27(12P13.1) WILD-TYPE 242 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     44   47
  DEL PEAK 27(12P13.1) WILD-TYPE  242  275
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  FEMALE                           44                            242
  MALE                             47                            275
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                     57
  DEL PEAK 27(12P13.1) WILD-TYPE                  324
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                               2
  DEL PEAK 27(12P13.1) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                      28
  DEL PEAK 27(12P13.1) WILD-TYPE                   118
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                                1
  DEL PEAK 27(12P13.1) WILD-TYPE                             12
D54V9, multiclass
                                clus
vv                               DEL PEAK 27(12P13.1) MUTATED
  COLON ADENOCARCINOMA                                     57
  COLON MUCINOUS ADENOCARCINOMA                             2
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 27(12P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      324
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                     118
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED     2  89
  DEL PEAK 27(12P13.1) WILD-TYPE   7 510
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED      2   89
  DEL PEAK 27(12P13.1) WILD-TYPE    7  510
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  NO                             2                              7
  YES                           89                            510
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.1) MUTATED    65   1   6   4
  DEL PEAK 27(12P13.1) WILD-TYPE 374   4  30  25
D54V11, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  R0                           65                            374
  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                          10    51
  DEL PEAK 27(12P13.1) WILD-TYPE                        50   241
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 27(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    50
  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    64  21
  DEL PEAK 28(12Q21.33) WILD-TYPE 404  94
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             85                             498 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             21                              94 
$`DEL PEAK 28(12Q21.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       43.76        24.33        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        56.25         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         5.79 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5256 
       22.42        16.44        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        49.08         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 
       65.85        36.72        36.00        12.00         8.42        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        10.98       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        28.57         0.66 
TCGA-G5-6233 
       18.28 

$`DEL PEAK 28(12Q21.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       42.90        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 
       16.57        37.05        37.25        37.02        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        29.19        33.53        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-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       29.00         0.99        21.01        24.00        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-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-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        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       38.99        36.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 
       24.00        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        25.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        38.04         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72        27.42 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       19.33        18.84        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        25.02        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        45.40        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 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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        13.25         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        67.30        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        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        13.05        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       32.98        31.30         9.70        70.03        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       17.23        13.55        19.10        37.74        10.39        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       20.02        10.39        86.63        65.98        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         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-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-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-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-A00H TCGA-AG-A011 TCGA-AG-A015 
       20.98        13.94         6.02        25.97        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-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         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        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        15.02        36.00        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-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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       37.51        31.30         0.39        32.19         0.69         0.53 
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 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                            0.2                             0.0 
  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 
                         17.950                          19.085 
[1] "0.2 - 129.3 (17.9)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.5"
D55V2, continuous
D55V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    60  27
  DEL PEAK 28(12Q21.33) WILD-TYPE 382 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     60   27
  DEL PEAK 28(12Q21.33) WILD-TYPE  382  135
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON                             60                             382
  RECTUM                            27                             135
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(12Q21.33) MUTATED        15        0        3        19         1
  DEL PEAK 28(12Q21.33) WILD-TYPE      89        1       33       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         68
                                 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         40       51        23         1
D55V4, multiclass
            clus
vv           DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  STAGE I                               15                              89
  STAGE IA                               0                               1
  STAGE II                               3                              33
  STAGE IIA                             19                             152
  STAGE IIB                              1                               9
  STAGE IIC                              2                               1
  STAGE III                              1                              25
  STAGE IIIA                             4                              17
  STAGE IIIB                            11                              68
  STAGE IIIC                            14                              40
  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  92 349  60
D55V5, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  T1                             3                              17
  T2                            15                              92
  T3                            64                             349
  T4                             6                              60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 28(12Q21.33) MUTATED    41  24  23
  DEL PEAK 28(12Q21.33) WILD-TYPE 301 125  91
D55V6, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  N0                            41                             301
  N1                            24                             125
  N2                            23                              91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    61  15
  DEL PEAK 28(12Q21.33) WILD-TYPE 387  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     61   15
  DEL PEAK 28(12Q21.33) WILD-TYPE  387   71
   clus
vv  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  0                            61                             387
  1                            15                              71
[1] 2 2
[1] FALSE
D55V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    39  49
  DEL PEAK 28(12Q21.33) WILD-TYPE 247 273
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     39   49
  DEL PEAK 28(12Q21.33) WILD-TYPE  247  273
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  FEMALE                            39                             247
  MALE                              49                             273
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                     57
  DEL PEAK 28(12Q21.33) WILD-TYPE                  324
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                               2
  DEL PEAK 28(12Q21.33) WILD-TYPE                            58
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                      26
  DEL PEAK 28(12Q21.33) WILD-TYPE                   120
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                                1
  DEL PEAK 28(12Q21.33) WILD-TYPE                             12
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                                       324
  COLON MUCINOUS ADENOCARCINOMA                               58
  RECTAL ADENOCARCINOMA                                      120
  RECTAL MUCINOUS ADENOCARCINOMA                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED     2  86
  DEL PEAK 28(12Q21.33) WILD-TYPE   7 513
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED      2   86
  DEL PEAK 28(12Q21.33) WILD-TYPE    7  513
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  NO                              2                               7
  YES                            86                             513
[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 369   5  33  26
D55V11, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  R0                            70                             369
  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                        52   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                                     52
  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  37
  DEL PEAK 29(14Q11.2) WILD-TYPE 306  78
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           199                            384 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                            37                             78 
$`DEL PEAK 29(14Q11.2) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
        4.80        43.76        42.28        35.11        16.57        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-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13        25.08        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3511 
       23.87        20.28        61.84         5.03         7.04         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        24.03        36.03        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       13.02        23.01        19.99        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       14.01        50.04        47.01        37.05        19.00        85.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 
       10.06        25.02        36.95        37.02        17.03        17.03 
TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.03        18.05        12.99        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L 
       50.99        34.06        26.01         7.96        34.03        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F 
       27.02        42.02        14.99        21.99        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J 
       31.00        33.04        26.01         2.96         2.01        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
        5.79        22.42        27.42        16.44        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
       15.75        17.85        18.84        75.25         1.41         5.65 
TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
       22.36        29.56         5.23         1.94         3.06         2.14 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
        0.07         0.26        49.08         2.01        25.02         8.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 
       11.08        10.06        45.40        12.26        13.51        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
        1.32        15.12        14.30        13.41        11.38        38.20 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 
       12.59       140.38         6.12        14.04       119.93        13.38 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 
       29.59        33.67        13.25         0.53        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       82.39        36.72        91.79        18.18        19.33        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       13.05        12.00        30.28        39.48        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       12.72        37.74        10.39        65.98        11.84        36.03 
TCGA-AG-3581 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 
        7.07        34.03        50.04         6.05         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
       19.99         1.02        17.03        35.01         1.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       36.03        14.04        17.03         6.02        25.97        23.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
        1.94        38.96        38.04         0.49        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         9.37         4.73        13.97         7.17        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97        36.00        10.98        13.05        10.06 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
      129.27        24.13        51.48        20.55        20.91        17.00 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 
       16.34        16.31        16.41        10.78        11.97        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.39        32.19         0.66         0.76        18.28        55.76 
TCGA-G5-6641 
       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 
       11.47        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       24.33        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 
       37.02        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        56.25 
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-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       17.95        29.95        20.98        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        36.00         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       14.93         0.00        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        29.98        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3973 
       26.01        24.00         2.01        20.98         2.01        13.05 
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-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       37.02        39.06        51.98        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-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-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72        10.88         0.20 
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-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
       17.82        17.26        19.33        50.37        58.39        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         3.19         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       19.59        11.51        20.19        20.42        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6298 
       16.31        16.24        35.41        19.43       107.67        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       47.15        52.80        10.98        19.33         9.93        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30         9.70 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 
       70.03        24.13        17.23        43.04        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3578 
       16.83        15.39        20.02        86.63        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
        2.01        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3887 
        7.99        29.98         1.02        32.98         0.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4007 
       13.02        14.01        48.03        32.02        19.99         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98        13.94        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98        49.97        61.97        41.00         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72        26.43         1.81         6.97        78.12 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       10.98        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
        5.29       126.44        41.36        57.24        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
        2.40        19.96        18.28        15.85        17.69         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57         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                           0.00 
  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 
                         18.05                          19.81 
[1] "0.1 - 140.4 (18.1)" "0.0 - 139.2 (19.8)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   136  68
  DEL PEAK 29(14Q11.2) WILD-TYPE 306  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    136   68
  DEL PEAK 29(14Q11.2) WILD-TYPE  306   94
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON                           136                            306
  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      72        1       25       116         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q11.2) MUTATED           1         9          9         29
  DEL PEAK 29(14Q11.2) WILD-TYPE         2        17         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         36       36        15         2
D56V4, multiclass
            clus
vv           DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            55                            116
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             9                             17
  STAGE IIIA                            9                             12
  STAGE IIIB                           29                             50
  STAGE IIIC                           18                             36
  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  18
  DEL PEAK 29(14Q11.2) WILD-TYPE  11  74 266  48
D56V5, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           33                             74
  T3                          147                            266
  T4                           18                             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   105  64  38
  DEL PEAK 29(14Q11.2) WILD-TYPE 237  85  76
D56V6, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  N0                          105                            237
  N1                           64                             85
  N2                           38                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   147  37
  DEL PEAK 29(14Q11.2) WILD-TYPE 301  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    147   37
  DEL PEAK 29(14Q11.2) WILD-TYPE  301   49
   clus
vv  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  0                          147                            301
  1                           37                             49
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED    97 110
  DEL PEAK 29(14Q11.2) WILD-TYPE 189 212
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED     97  110
  DEL PEAK 29(14Q11.2) WILD-TYPE  189  212
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  FEMALE                           97                            189
  MALE                            110                            212
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                    130
  DEL PEAK 29(14Q11.2) WILD-TYPE                  251
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                               5
  DEL PEAK 29(14Q11.2) WILD-TYPE                            55
                                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                                    130
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      251
  COLON MUCINOUS ADENOCARCINOMA                              55
  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     4 203
  DEL PEAK 29(14Q11.2) WILD-TYPE   5 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED      4  203
  DEL PEAK 29(14Q11.2) WILD-TYPE    5  396
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  NO                             4                              5
  YES                          203                            396
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(14Q11.2) MUTATED   146   2  10  10
  DEL PEAK 29(14Q11.2) WILD-TYPE 293   3  26  19
D56V11, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  R0                          146                            293
  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                          20   101
  DEL PEAK 29(14Q11.2) WILD-TYPE                        40   191
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     101
                                  clus
vv                                 DEL PEAK 29(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    40
  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  36
  DEL PEAK 30(14Q31.1) WILD-TYPE 302  79
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           202                            381 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                            36                             79 
$`DEL PEAK 30(14Q31.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
        4.80        43.76        42.28        35.11        45.60        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 
       23.61        22.52        24.13        25.08        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 
       21.76        24.69        23.87        20.28        61.84         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3526 TCGA-AA-3530 
        6.97        38.99         9.07        24.03        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       34.03        13.02        23.01        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01        15.02        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05        10.06        25.02        36.95        37.02        17.03 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       31.07        17.03        24.03        18.05         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       24.00         7.96        38.04        27.02        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       21.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       16.44        14.50         0.95        15.75         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
       18.84        75.25         1.41         5.65        22.36        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
        5.23         1.94         3.06         2.14         0.07         0.26 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 
       49.08         2.01        25.02         8.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       29.03        13.02        15.02        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       45.40        12.26        13.51        18.25         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 
       14.30        13.41        11.38        38.20        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28H TCGA-F4-6460 
        7.50       131.51        14.04       119.93       117.07        13.38 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 
       29.59        33.67        13.25         0.53         8.35        82.39 
TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 
       36.72        91.79        18.18        19.33        15.65        13.05 
TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-A56L 
       12.00        30.28        39.48        13.55        37.74        65.98 
TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       11.84        36.03        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 
        6.05         0.99         1.02         0.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       35.01         1.02        48.03        36.03        14.04        17.03 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G 
        6.02        25.97        23.01        70.03         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
       38.04         0.49        10.19         6.05         6.05         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        4.73        13.97         7.17        10.98        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        10.98        13.05        10.06       129.27 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       51.48        20.55        17.00        16.34        16.31        16.41 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        11.97        31.30         0.39        32.19         0.66 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.76        18.28        55.76        26.43 

$`DEL PEAK 30(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       11.47        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       24.33        44.91        13.94        37.05        37.25        37.02 
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        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 
       63.98         1.02        13.02         1.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        8.05         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-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-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
        6.97        54.02         0.92        47.05        11.01         5.98 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       34.03         2.01        13.05        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       18.05        18.05         4.01         0.99        17.03        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72        10.88         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 
       16.31        21.44        17.82        17.26        19.33        50.37 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       58.39        32.94         5.13        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.19         2.24         3.25         3.29         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       11.01        12.03        19.59        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43       130.65        92.75        49.91        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37        35.97        60.79        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.31        16.24        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       55.04        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        19.33         9.93 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
        9.70        70.03        24.13        17.23        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       10.39        86.63        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 
        7.07        20.05        24.00         1.02         2.01         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99        19.99         7.99        29.98        32.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 
        0.99        19.99        36.95        13.02        14.01        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        28.04         1.02         0.99        20.98        13.94 
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-A02N 
       31.00        64.01        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
        6.97        78.12        15.02        12.00        15.02        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-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         0.49         2.40        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
       15.85        17.69         8.61        11.51        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 
        8.45         9.96        37.51        28.57         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        1.12         0.46        47.08 

  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                         17.44                          19.99 
[1] "0.1 - 140.4 (17.4)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   143  68
  DEL PEAK 30(14Q31.1) WILD-TYPE 299  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    143   68
  DEL PEAK 30(14Q31.1) WILD-TYPE  299   94
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON                           143                            299
  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      72        1       27       113         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(14Q31.1) MUTATED           1        10          9         30
  DEL PEAK 30(14Q31.1) WILD-TYPE         2        16         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         35       34        15         1
D57V4, multiclass
            clus
vv           DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            58                            113
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            9                             12
  STAGE IIIB                           30                             49
  STAGE IIIC                           19                             35
  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  18
  DEL PEAK 30(14Q31.1) WILD-TYPE  11  74 260  48
D57V5, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  T1                            9                             11
  T2                           33                             74
  T3                          153                            260
  T4                           18                             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   106  65  42
  DEL PEAK 30(14Q31.1) WILD-TYPE 236  84  72
D57V6, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  N0                          106                            236
  N1                           65                             84
  N2                           42                             72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   151  41
  DEL PEAK 30(14Q31.1) WILD-TYPE 297  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    151   41
  DEL PEAK 30(14Q31.1) WILD-TYPE  297   45
   clus
vv  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  0                          151                            297
  1                           41                             45
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED    94 119
  DEL PEAK 30(14Q31.1) WILD-TYPE 192 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED     94  119
  DEL PEAK 30(14Q31.1) WILD-TYPE  192  203
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  FEMALE                           94                            192
  MALE                            119                            203
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                    137
  DEL PEAK 30(14Q31.1) WILD-TYPE                  244
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                               5
  DEL PEAK 30(14Q31.1) WILD-TYPE                            55
                                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                                    137
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      244
  COLON MUCINOUS ADENOCARCINOMA                              55
  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     2 211
  DEL PEAK 30(14Q31.1) WILD-TYPE   7 388
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED      2  211
  DEL PEAK 30(14Q31.1) WILD-TYPE    7  388
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  NO                             2                              7
  YES                          211                            388
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(14Q31.1) MUTATED   146   2  15  10
  DEL PEAK 30(14Q31.1) WILD-TYPE 293   3  21  19
D57V11, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  R0                          146                            293
  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                          21   100
  DEL PEAK 30(14Q31.1) WILD-TYPE                        39   192
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 30(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     100
                                  clus
vv                                 DEL PEAK 30(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    39
  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   191  45
  DEL PEAK 31(15Q11.2) WILD-TYPE 277  70
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           236                            347 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                            45                             70 
$`DEL PEAK 31(15Q11.2) MUTATED`
TCGA-4N-A93T TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
        4.80        43.76        43.43        24.33        42.28        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       45.60        16.57        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-A6-A56B TCGA-AA-3488 
       21.76        20.12        20.28        61.84        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        7.04         1.02         6.97        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-3685 
       19.99        19.99         2.01        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05         1.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        36.03         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 
       17.03        24.03        27.02        29.98        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       21.99        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-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-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       15.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        2.96        41.00         5.79        22.42        27.42        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D 
        0.46        14.50        16.31         0.95        15.75        17.85 
TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 
       18.84        83.80        65.00        62.79        61.41        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        5.23         3.19         2.14         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       49.08         2.01        25.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 
       12.03        12.26        20.19        17.75         1.32        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 
       17.13        12.49         7.53        10.13         9.04        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 
      131.51         6.12        14.04        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        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 
       35.41        28.21         8.35        67.30        65.85        55.04 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       45.11        36.72        36.00        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       19.33        12.79        29.46         9.70        30.28        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L 
       43.04        13.55        37.74        14.50        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 
       11.84        32.02        36.03        20.05        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 
        6.05        19.99        29.98         0.99        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       35.01         1.02        19.99        28.04        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
       13.94        25.97        23.01        37.02         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       64.01         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         7.17 
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-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-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        28.57        32.19         0.66         0.69 
TCGA-G5-6233 TCGA-G5-6641 
       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 
       11.47        11.47        43.76        46.65        42.90        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 
       13.94        37.05        37.25        37.02        14.53        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
        8.05        19.07         0.00        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       26.01         0.99        17.95        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
        0.92        47.05        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 
       25.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3875 
       33.07         0.00        32.05        31.07        53.00        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-3977 TCGA-AA-3986 
        2.01        20.98        34.03        16.08        25.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        38.04         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       34.98        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-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        10.88         0.20         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
        0.20        21.44        17.82        17.26        19.33        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        26.04         8.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.95        45.40        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85         4.80        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.39        12.43        14.30         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       49.91        44.32       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64        13.45         6.18        16.31        29.59 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6304 
       19.43       107.67        82.39        23.51        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        51.75        39.42        35.93        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       18.18        19.33         9.93        15.65        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 
       42.77        32.98         8.42        31.30        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.23        19.10        12.72        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        86.63        36.03        12.00         8.02         7.07 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       24.00         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99         1.02        32.98 
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-A020 
       15.95        36.03         9.07        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       51.98        49.97        61.97         1.45         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
        1.81         6.05         6.97        13.97        78.12        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       11.01        15.02        12.00        15.02        10.98        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.95         5.29       126.44        32.61        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-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 
       17.46         8.45         9.96        37.51         0.39         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                          0.26                           0.00 
  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 
                         19.99                          18.28 
[1] "0.3 - 140.4 (20.0)" "0.0 - 139.2 (18.3)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   172  74
  DEL PEAK 31(15Q11.2) WILD-TYPE 270  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    172   74
  DEL PEAK 31(15Q11.2) WILD-TYPE  270   88
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  COLON                           172                            270
  RECTUM                           74                             88
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q11.2) MUTATED        39        0        9        63         3
  DEL PEAK 31(15Q11.2) WILD-TYPE      65        1       27       108         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q11.2) MUTATED           2         8         12         34
  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           28       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                              39                             65
  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                           34                             45
  STAGE IIIC                           28                             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  40 174  26
  DEL PEAK 31(15Q11.2) WILD-TYPE  11  67 239  40
D58V5, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           40                             67
  T3                          174                            239
  T4                           26                             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   123  72  54
  DEL PEAK 31(15Q11.2) WILD-TYPE 219  77  60
D58V6, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  N0                          123                            219
  N1                           72                             77
  N2                           54                             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"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   175  45
  DEL PEAK 31(15Q11.2) WILD-TYPE 273  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    175   45
  DEL PEAK 31(15Q11.2) WILD-TYPE  273   41
   clus
vv  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  0                          175                            273
  1                           45                             41
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   112 137
  DEL PEAK 31(15Q11.2) WILD-TYPE 174 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    112  137
  DEL PEAK 31(15Q11.2) WILD-TYPE  174  185
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  FEMALE                          112                            174
  MALE                            137                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                    155
  DEL PEAK 31(15Q11.2) WILD-TYPE                  226
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              16
  DEL PEAK 31(15Q11.2) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                      67
  DEL PEAK 31(15Q11.2) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                6
  DEL PEAK 31(15Q11.2) WILD-TYPE                              7
D58V9, multiclass
                                clus
vv                               DEL PEAK 31(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    155
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    67
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 31(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      226
  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     7 242
  DEL PEAK 31(15Q11.2) WILD-TYPE   2 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED      7  242
  DEL PEAK 31(15Q11.2) WILD-TYPE    2  357
     clus
vv    DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  NO                             7                              2
  YES                          242                            357
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q11.2) MUTATED   176   2  15   9
  DEL PEAK 31(15Q11.2) WILD-TYPE 263   3  21  20
D58V11, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  R0                          176                            263
  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                          22   127
  DEL PEAK 31(15Q11.2) WILD-TYPE                        38   165
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     127
                                  clus
vv                                 DEL PEAK 31(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    38
  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   190  44
  DEL PEAK 32(15Q15.2) WILD-TYPE 278  71
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           234                            349 
  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                            44                             71 
$`DEL PEAK 32(15Q15.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       42.28        44.91        45.60        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 
       32.45        32.91        30.44        29.19        29.16        22.52 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 
       25.08        20.61        21.76        20.12        20.28        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       56.25         5.03         7.04         1.02         6.97         9.07 
TCGA-AA-3522 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       37.05        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 
       24.00        23.01        19.99        19.99         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01        11.01        37.05        19.00        36.00        85.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       36.03         0.99        31.07        17.03        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       12.99         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
       24.00        27.02        19.00        34.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       14.99        15.02        15.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        2.96        41.00         5.79        22.42        27.42        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       14.50        16.31         0.95        15.75         0.20        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       19.33        18.84        83.80        65.00        62.79        61.41 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 
       29.56         5.23         3.19         2.14         0.26       102.44 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       49.08         2.01        25.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 
       12.03        12.26        20.19         1.32        15.12         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.13         9.04        13.41        11.38       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F 
       13.32        12.59       140.38       131.51         6.12        35.97 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
       95.18        13.38        35.87         1.55        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 
       13.25         0.53        35.41        28.21         8.35        65.85 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 
       55.04        45.11        36.72        36.00        26.04        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D 
       46.75        10.98        19.33        12.79        29.46         9.70 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 
       30.28        24.13        43.04        13.55        37.74        14.50 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       10.39        65.98        11.84        32.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3727 
       24.00        46.03        34.03         6.05        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 
       29.98        32.98         0.99        19.99        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
        1.02        19.99        28.04        14.04        17.03        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 
       25.97        23.01        37.02         1.02        12.00         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       38.96        41.00        38.04         0.49         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        6.05         9.37         4.73         7.17        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       36.00        13.05        10.06        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 
       51.48         0.49         2.40        15.85        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 
        8.61        11.51        10.78        13.64        11.97        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
       28.57        32.19         0.66         0.69        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 
       11.47        46.65        42.90        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        37.02        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-3529 
        1.02        24.03        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        34.03        29.00        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        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
       15.95        14.93         0.00         0.00         0.00        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 
       38.04         4.01        27.02         0.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72        10.88         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
       27.09        21.44        17.82        17.26        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41         6.77        12.10       100.01        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         3.25         3.29         0.07         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        26.04         8.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.95        45.40        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        43.27        17.85         4.80        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-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       24.43        38.20        49.91         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-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-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       13.45         6.18        16.31        29.59        19.43       107.67 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 
       51.75        39.42        35.93        26.43        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        18.18        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        13.05        12.00        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 
        8.42        31.30        70.03        39.48        17.23        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        10.39        16.83        15.39        20.02        86.63 
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-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02         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-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       64.01        10.98        51.98        49.97        61.97         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        0.72        26.43         1.81         6.05         6.97        13.97 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       78.12        10.98        11.01        15.02        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       10.98        30.05        12.95         5.29       126.44       129.27 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       17.69        16.34        17.46         8.45         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.39         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE 
                           0.2                            0.0 
  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 
                         19.99                          18.28 
[1] "0.2 - 140.4 (20.0)" "0.0 - 139.2 (18.3)"
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   167  77
  DEL PEAK 32(15Q15.2) WILD-TYPE 275  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    167   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                           167                            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        41        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         34
  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           27       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                              41                             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                           34                             45
  STAGE IIIC                           27                             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  41 172  25
  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                           41                             66
  T3                          172                            241
  T4                           25                             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   120  75  52
  DEL PEAK 32(15Q15.2) WILD-TYPE 222  74  62
D59V6, multiclass
    clus
vv   DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  N0                          120                            222
  N1                           75                             74
  N2                           52                             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"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   169  47
  DEL PEAK 32(15Q15.2) WILD-TYPE 279  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    169   47
  DEL PEAK 32(15Q15.2) WILD-TYPE  279   39
   clus
vv  DEL PEAK 32(15Q15.2) MUTATED DEL PEAK 32(15Q15.2) WILD-TYPE
  0                          169                            279
  1                           47                             39
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.2) MUTATED   110 137
  DEL PEAK 32(15Q15.2) WILD-TYPE 176 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED    110  137
  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                          110                            176
  MALE                            137                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                    151
  DEL PEAK 32(15Q15.2) WILD-TYPE                  230
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                              15
  DEL PEAK 32(15Q15.2) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                      70
  DEL PEAK 32(15Q15.2) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.2) MUTATED                                6
  DEL PEAK 32(15Q15.2) WILD-TYPE                              7
D59V9, multiclass
                                clus
vv                               DEL PEAK 32(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            15
  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     7 240
  DEL PEAK 32(15Q15.2) WILD-TYPE   2 359
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.2) MUTATED      7  240
  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                          240                            359
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q15.2) MUTATED   177   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                          177                            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                          24   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                                  24
  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   189  42
  DEL PEAK 33(15Q21.1) WILD-TYPE 279  73
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                           231                            352 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                            42                             73 
$`DEL PEAK 33(15Q21.1) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        4.80        43.76        43.76        43.43        42.90        24.33 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       44.91        45.60        16.57        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.91        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 
       20.61        21.76        20.12        20.28        61.84         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 
        7.04         1.02         6.97         9.07        37.05        29.00 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02         0.00        17.03        10.06        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
       36.03         0.99        31.07        17.03        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       12.99         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q 
       24.00        27.02        19.00        30.02        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         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       16.44        14.50        15.75         0.20        17.85        18.84 
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        49.08         2.01 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
       25.02        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        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       35.41         8.35        65.85        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       36.00        26.04        91.79        46.75        10.98        19.33 
TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 
       12.79        29.46         9.70        30.28        24.13        43.04 
TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N 
       13.55        37.74        14.50        10.39        65.98        11.84 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
       32.02        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
        6.05        19.99         0.99        29.98        32.98         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-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        12.00         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
        0.49         0.69        10.19         6.05         9.37         4.73 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
        7.17        12.99        13.97        36.00        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        24.13        51.48         0.49         2.40 
TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        31.30        28.57        32.19         0.66 
TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.69        18.28        26.43 

$`DEL PEAK 33(15Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 
       11.47        11.47        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        37.02        14.53        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 
       19.66        16.24        24.92        56.25         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-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
       19.07         0.00        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-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        15.02         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
       17.98        15.95        14.93         0.00         0.00        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-A00J TCGA-AA-A00K TCGA-AA-A00L 
       27.02        13.94        38.04        18.05        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        4.01        27.02         0.99        21.99        34.98        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72        10.88         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       16.31         0.95        21.44        17.82        17.26        19.33 
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        45.40        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        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 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-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       19.43       107.67        28.21        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 
       67.30        53.62        44.68        51.75        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       26.43        22.09        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80        18.18        19.33         9.93        15.65        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       12.00        42.77        32.98         8.42        31.30        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       39.48        17.23        19.10        12.72        10.39        16.83 
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-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        7.07         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 
       15.95        19.99         7.99         1.02         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 
       36.95        13.02        14.01        48.03        32.02        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 
        1.02         0.99        20.98         6.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         1.45         0.72        26.43         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
        6.05         6.97        13.97        78.12        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.00        15.02        10.98        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
        5.29       126.44       129.27        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 
       20.91        17.00        18.28        17.69        16.34        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        8.45         9.96        37.51         0.39         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 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE 
                        19.990                         18.265 
[1] "0.0 - 140.4 (20.0)" "0.0 - 139.2 (18.3)"
[1] "hr=" "1.1"
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   165  77
  DEL PEAK 33(15Q21.1) WILD-TYPE 277  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    165   77
  DEL PEAK 33(15Q21.1) WILD-TYPE  277   85
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  COLON                           165                            277
  RECTUM                           77                             85
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q21.1) MUTATED        38        0        8        63         4
  DEL PEAK 33(15Q21.1) WILD-TYPE      66        1       28       108         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q21.1) MUTATED           2         9         10         32
  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           26       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                              38                             66
  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                           32                             47
  STAGE IIIC                           26                             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  39 171  26
  DEL PEAK 33(15Q21.1) WILD-TYPE  12  68 242  40
D60V5, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  T1                            8                             12
  T2                           39                             68
  T3                          171                            242
  T4                           26                             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   121  72  51
  DEL PEAK 33(15Q21.1) WILD-TYPE 221  77  63
D60V6, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  N0                          121                            221
  N1                           72                             77
  N2                           51                             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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   168  46
  DEL PEAK 33(15Q21.1) WILD-TYPE 280  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    168   46
  DEL PEAK 33(15Q21.1) WILD-TYPE  280   40
   clus
vv  DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  0                          168                            280
  1                           46                             40
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q21.1) MUTATED   107 137
  DEL PEAK 33(15Q21.1) WILD-TYPE 179 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED    107  137
  DEL PEAK 33(15Q21.1) WILD-TYPE  179  185
        clus
vv       DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  FEMALE                          107                            179
  MALE                            137                            185
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                    149
  DEL PEAK 33(15Q21.1) WILD-TYPE                  232
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                              15
  DEL PEAK 33(15Q21.1) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                      70
  DEL PEAK 33(15Q21.1) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q21.1) MUTATED                                6
  DEL PEAK 33(15Q21.1) WILD-TYPE                              7
D60V9, multiclass
                                clus
vv                               DEL PEAK 33(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    149
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 33(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      232
  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     7 237
  DEL PEAK 33(15Q21.1) WILD-TYPE   2 362
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q21.1) MUTATED      7  237
  DEL PEAK 33(15Q21.1) WILD-TYPE    2  362
     clus
vv    DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  NO                             7                              2
  YES                          237                            362
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q21.1) MUTATED   175   1  16   8
  DEL PEAK 33(15Q21.1) WILD-TYPE 264   4  20  21
D60V11, multiclass
    clus
vv   DEL PEAK 33(15Q21.1) MUTATED DEL PEAK 33(15Q21.1) WILD-TYPE
  R0                          175                            264
  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                          20   122
  DEL PEAK 33(15Q21.1) WILD-TYPE                        40   170
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     122
                                  clus
vv                                 DEL PEAK 33(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    40
  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   181  42
  DEL PEAK 34(15Q22.33) WILD-TYPE 287  73
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            223                             360 
  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                             42                              73 
$`DEL PEAK 34(15Q22.33) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        4.80        43.76        43.76        43.43        24.33        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       45.60        16.57        34.65        36.53        32.45        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-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       20.28        61.84         5.03         7.04         1.02         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
        9.07        37.05        29.00        12.99        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 
       13.02        23.01        19.99        19.99         2.01        50.04 
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-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        17.03        10.06         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.03        29.98        12.99         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F 
       13.05        34.06        24.00        27.02        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K 
       42.02        17.03        14.99        15.02        15.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 
       15.75         0.20        17.85        18.84        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        49.08         2.01        25.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       13.02        29.06         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       29.03        16.04        15.02        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       10.06        12.03        20.19         1.32        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       12.49         7.53        10.13         9.04        13.41        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      131.51         6.12        14.04        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        13.25         0.53        35.41 
TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 
        8.35        65.85        55.04        45.11        36.72        36.00 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW 
       91.79        46.75        10.98        19.33        12.79        29.46 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
        8.42         9.70        30.28        24.13        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       12.72        37.74        14.50        10.39        65.98        32.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 
       36.03        20.05        24.00        34.03         6.05        15.95 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 
       19.99        29.98         0.99        19.99        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
        1.02        19.99        28.04        14.04        17.03        13.94 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       25.97        23.01        37.02         1.02        12.00        70.03 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       38.96        41.00        38.04         0.49         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 
        6.05         9.37         7.17        10.98        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       36.00        13.05        10.06        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 
       24.13        51.48         0.49         2.40        15.85        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 
       16.41        11.51        10.78        13.64        11.97        31.30 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 
       28.57        32.19         0.66         0.69         0.46        18.28 
TCGA-G5-6641 
       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 
       11.47        11.47        46.65        42.90        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        37.02        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 
       56.25         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-3529 TCGA-AA-3530 
       24.03        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 
       34.03        29.00        26.01         0.99        14.01        24.00 
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-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        14.93         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       33.07         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-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-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       26.01        25.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F 
       27.02         0.99        21.99        34.98        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-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-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       10.88         0.20         0.92        27.09        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        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-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       17.75        18.25        43.27        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
        7.50        44.32       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        13.64        13.45         6.18        16.31 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       29.59        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        67.30        53.62        44.68        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        47.15        52.80        18.18        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       15.65        13.05        12.00        42.77        32.98        31.30 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 
       70.03        39.48        17.23        19.10        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       15.39        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        8.02         7.07         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       12.03         0.99        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-A01Y 
        6.02        15.95        36.03         9.07        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AH-6547 
       10.98        51.98        49.97         1.94        61.97         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.72        26.43         1.81         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       13.97        78.12        11.01        15.02        12.00        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 
       10.98        30.05        12.95         5.29       126.44        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-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       16.34         8.61        17.46         8.45         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.39         0.53         1.12         0.76        55.76        47.08 

  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE 
                            0.2                             0.0 
  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 
                          19.00                           19.07 
[1] "0.2 - 140.4 (19.0)" "0.0 - 139.2 (19.1)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   156  75
  DEL PEAK 34(15Q22.33) WILD-TYPE 286  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    156   75
  DEL PEAK 34(15Q22.33) WILD-TYPE  286   87
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  COLON                            156                             286
  RECTUM                            75                              87
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(15Q22.33) MUTATED        32        0        7        60         3
  DEL PEAK 34(15Q22.33) WILD-TYPE      72        1       29       111         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q22.33) MUTATED           2         7         11         32
  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           29       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                               32                              72
  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                            32                              47
  STAGE IIIC                            29                              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  31 171  23
  DEL PEAK 34(15Q22.33) WILD-TYPE  11  76 242  43
D61V5, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  T1                             9                              11
  T2                            31                              76
  T3                           171                             242
  T4                            23                              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   111  69  54
  DEL PEAK 34(15Q22.33) WILD-TYPE 231  80  60
D61V6, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  N0                           111                             231
  N1                            69                              80
  N2                            54                              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"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   159  45
  DEL PEAK 34(15Q22.33) WILD-TYPE 289  41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    159   45
  DEL PEAK 34(15Q22.33) WILD-TYPE  289   41
   clus
vv  DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  0                           159                             289
  1                            45                              41
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 34(15Q22.33) MUTATED   105 129
  DEL PEAK 34(15Q22.33) WILD-TYPE 181 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED    105  129
  DEL PEAK 34(15Q22.33) WILD-TYPE  181  193
        clus
vv       DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  FEMALE                           105                             181
  MALE                             129                             193
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                    141
  DEL PEAK 34(15Q22.33) WILD-TYPE                  240
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                              14
  DEL PEAK 34(15Q22.33) WILD-TYPE                            46
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                      68
  DEL PEAK 34(15Q22.33) WILD-TYPE                    78
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q22.33) MUTATED                                6
  DEL PEAK 34(15Q22.33) WILD-TYPE                              7
D61V9, multiclass
                                clus
vv                               DEL PEAK 34(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                     141
  COLON MUCINOUS ADENOCARCINOMA                             14
  RECTAL ADENOCARCINOMA                                     68
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 34(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       240
  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     8 226
  DEL PEAK 34(15Q22.33) WILD-TYPE   1 373
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(15Q22.33) MUTATED      8  226
  DEL PEAK 34(15Q22.33) WILD-TYPE    1  373
     clus
vv    DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  NO                              8                               1
  YES                           226                             373
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 34(15Q22.33) MUTATED   167   1  15   8
  DEL PEAK 34(15Q22.33) WILD-TYPE 272   4  21  21
D61V11, multiclass
    clus
vv   DEL PEAK 34(15Q22.33) MUTATED DEL PEAK 34(15Q22.33) WILD-TYPE
  R0                           167                             272
  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                          20   124
  DEL PEAK 34(15Q22.33) WILD-TYPE                        40   168
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 34(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      124
                                  clus
vv                                 DEL PEAK 34(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     40
  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 425  95
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            63                            520 
  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                            20                             95 
$`DEL PEAK 35(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 
       24.33        44.91        45.60        34.65        14.53        21.76 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 
       61.84         5.03        13.02        54.02        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 
       36.95        31.07         2.01        33.01         2.01         2.01 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F TCGA-AA-A02Y TCGA-AD-A5EK 
       27.02        34.03        27.02        39.98        39.98        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
        0.46        14.50        16.31         0.20        17.85         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 
       18.18        10.98        42.77        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 
       32.19         0.53        18.28 

$`DEL PEAK 35(16P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.43        42.90        42.28        35.11        13.94        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
        8.38        25.08        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       37.05        36.03         8.05        19.07         0.00        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-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-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97         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-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        37.02        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05        31.00        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        24.00        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
       22.42        27.42        10.88         0.20         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        15.75        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       18.84        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        49.08 
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        25.02        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        45.40        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 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         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 
       13.25         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        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        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        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       19.33         9.93        15.65        12.79        13.05        12.00 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       29.46        32.98         8.42        31.30         9.70        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        19.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        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        10.98        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       28.57         0.39         0.66         0.69         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE 
                           0.2                            0.0 
  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 
                        18.180                         19.085 
[1] "0.2 - 61.8 (18.2)"  "0.0 - 140.4 (19.1)"
[1] "hr=" "2"  
D62V2, continuous
D62V3, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    54  13
  DEL PEAK 35(16P13.3) WILD-TYPE 388 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     54   13
  DEL PEAK 35(16P13.3) WILD-TYPE  388  149
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  COLON                            54                            388
  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     100        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         70
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(16P13.3) MUTATED           11        8         5         0
  DEL PEAK 35(16P13.3) WILD-TYPE         43       53        22         2
D62V4, multiclass
            clus
vv           DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  STAGE I                               4                            100
  STAGE IA                              0                              1
  STAGE II                              3                             33
  STAGE IIA                            23                            148
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             0                             26
  STAGE IIIA                            0                             21
  STAGE IIIB                            9                             70
  STAGE IIIC                           11                             43
  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  20 101 359  59
D62V5, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  T1                            0                             20
  T2                            6                            101
  T3                           54                            359
  T4                            7                             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 35(16P13.3) MUTATED    33  16  18
  DEL PEAK 35(16P13.3) WILD-TYPE 309 133  96
D62V6, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  N0                           33                            309
  N1                           16                            133
  N2                           18                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    45  13
  DEL PEAK 35(16P13.3) WILD-TYPE 403  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     45   13
  DEL PEAK 35(16P13.3) WILD-TYPE  403   73
   clus
vv  DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  0                           45                            403
  1                           13                             73
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED    30  37
  DEL PEAK 35(16P13.3) WILD-TYPE 256 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED     30   37
  DEL PEAK 35(16P13.3) WILD-TYPE  256  285
        clus
vv       DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  FEMALE                           30                            256
  MALE                             37                            285
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                     47
  DEL PEAK 35(16P13.3) WILD-TYPE                  334
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                               7
  DEL PEAK 35(16P13.3) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                      10
  DEL PEAK 35(16P13.3) WILD-TYPE                   136
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16P13.3) MUTATED                                2
  DEL PEAK 35(16P13.3) WILD-TYPE                             11
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                                      334
  COLON MUCINOUS ADENOCARCINOMA                              53
  RECTAL ADENOCARCINOMA                                     136
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(16P13.3) MUTATED     0  67
  DEL PEAK 35(16P13.3) WILD-TYPE   9 532
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16P13.3) MUTATED      0   67
  DEL PEAK 35(16P13.3) WILD-TYPE    9  532
     clus
vv    DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  NO                             0                              9
  YES                           67                            532
[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 389   4  32  28
D62V11, multiclass
    clus
vv   DEL PEAK 35(16P13.3) MUTATED DEL PEAK 35(16P13.3) WILD-TYPE
  R0                           50                            389
  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                        50   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                                    50
  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 410  96
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            77                            506 
  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                            19                             96 
$`DEL PEAK 36(16Q23.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-5660 TCGA-A6-5661 
       43.76        42.90        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        16.44        17.85 
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        18.18 
TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 
       10.98        31.30        30.28        10.39        32.02        36.03 
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        32.19         0.53        18.28 

$`DEL PEAK 36(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        46.65        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       24.33        44.91        35.11        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        37.02        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        31.63        30.44        23.61        22.09        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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       24.16        20.61        24.69        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        7.04         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-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-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-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        19.04        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3841 
       35.05         0.99        25.02         1.02        15.95        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       37.02        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       33.07         0.00        32.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        19.00        34.03        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        5.79        22.42        27.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
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        49.08 
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        25.02        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        45.40        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        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         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        13.25 
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        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        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 
       19.33        19.33         9.93        15.65        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       12.00        42.77        29.46        32.98         8.42         9.70 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       19.10        12.72        37.74        10.39        14.50        16.83 
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-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       15.95        19.99         0.99        29.98         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         1.45         0.69        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         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        78.12         7.17        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        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       17.69        16.34        16.31        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       13.64        17.46        37.51        31.30        28.57         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 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE 
                          0.49                           0.00 
  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 
                         17.85                          19.33 
[1] "0.5 - 129.3 (17.9)" "0.0 - 140.4 (19.3)"
[1] "hr=" "1.7"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    58  23
  DEL PEAK 36(16Q23.1) WILD-TYPE 384 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     58   23
  DEL PEAK 36(16Q23.1) WILD-TYPE  384  139
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  COLON                            58                            384
  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      91        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         71
                                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         48       51        22         2
D63V4, multiclass
            clus
vv           DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  STAGE I                              13                             91
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            24                            147
  STAGE IIB                             2                              8
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            0                             21
  STAGE IIIB                            8                             71
  STAGE IIIC                            6                             48
  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  93 358  54
D63V5, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  T1                            0                             20
  T2                           14                             93
  T3                           55                            358
  T4                           12                             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 36(16Q23.1) MUTATED    47  16  17
  DEL PEAK 36(16Q23.1) WILD-TYPE 295 133  97
D63V6, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  N0                           47                            295
  N1                           16                            133
  N2                           17                             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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    57  14
  DEL PEAK 36(16Q23.1) WILD-TYPE 391  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     57   14
  DEL PEAK 36(16Q23.1) WILD-TYPE  391   72
   clus
vv  DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  0                           57                            391
  1                           14                             72
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED    42  39
  DEL PEAK 36(16Q23.1) WILD-TYPE 244 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED     42   39
  DEL PEAK 36(16Q23.1) WILD-TYPE  244  283
        clus
vv       DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  FEMALE                           42                            244
  MALE                             39                            283
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                     48
  DEL PEAK 36(16Q23.1) WILD-TYPE                  333
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                              10
  DEL PEAK 36(16Q23.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                      20
  DEL PEAK 36(16Q23.1) WILD-TYPE                   126
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16Q23.1) MUTATED                                2
  DEL PEAK 36(16Q23.1) WILD-TYPE                             11
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                                      333
  COLON MUCINOUS ADENOCARCINOMA                              50
  RECTAL ADENOCARCINOMA                                     126
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(16Q23.1) MUTATED     1  80
  DEL PEAK 36(16Q23.1) WILD-TYPE   8 519
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16Q23.1) MUTATED      1   80
  DEL PEAK 36(16Q23.1) WILD-TYPE    8  519
     clus
vv    DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  NO                             1                              8
  YES                           80                            519
[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 383   5  33  25
D63V11, multiclass
    clus
vv   DEL PEAK 36(16Q23.1) MUTATED DEL PEAK 36(16Q23.1) WILD-TYPE
  R0                           56                            383
  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                        49   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                                    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(64) Variable = DEL PEAK 37(17P12) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 37(17P12) MUTATED   278  69
  DEL PEAK 37(17P12) WILD-TYPE 190  46
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                         347                          236 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                          69                           46 
$`DEL PEAK 37(17P12) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
       11.47         4.80        43.76        43.76        43.43        24.33 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        14.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       29.19        32.71        29.16        27.09        22.52        24.13 
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-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       61.84         5.03         7.04         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       36.03        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       47.01         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       10.06        25.02        38.99        36.95        37.02        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       33.07        32.05         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3952 
       27.02        29.98        18.05         2.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       38.04        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
       15.02        10.98        32.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       33.04        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
       41.00        40.96        21.37         4.21         0.79         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42         0.20        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 
       16.31         0.95        15.75         0.20        17.85        75.25 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65         5.13        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       61.41        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
      102.44        49.08        21.99         2.01        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 
       27.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       15.02        17.03        29.03        21.99        14.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       15.02        11.01        13.05        11.08        10.06        45.40 
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-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
        1.32        43.27        15.12        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
       12.59       140.38        44.32       131.51       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 
       14.04        26.47       119.93        35.97       117.07        13.38 
TCGA-F4-6461 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 
       11.11        16.31        16.24        33.67        13.25         8.35 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       23.51        65.85        44.68        55.04        45.11        39.42 
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-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        19.33         9.93        15.65        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       12.00        42.77        29.46        32.98         8.42         9.70 
TCGA-RU-A8FL TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       30.28        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        37.74        14.50        15.39        20.02        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-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
        1.02        32.98         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       70.03        64.01        51.98         1.94        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.05         6.97        13.97         7.17        10.98        11.01 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02        10.98        30.05        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       51.48         0.49         2.40        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 
       17.69        16.34        16.31        16.41        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        28.57         0.39 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         0.76         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 
       11.47        46.65        42.90        44.91        13.94        37.02 
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        56.25         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-3529 
       63.98        13.02         1.02         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 
       19.07        34.03        29.00        26.01         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       29.95        20.98         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02        11.01         5.03        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 
       35.05         0.99         1.02        17.98        15.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3860 
        0.00        17.03         0.00         0.00        36.03        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00        12.99        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
        2.01        13.05        25.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       34.98        15.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R 
       35.01        26.01        39.06        51.98         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       39.98        18.05         0.07        56.55         0.72        10.88 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.92        27.09        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 
       18.84        50.37        58.39        32.94        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01        11.74         3.06         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 
       26.04        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       12.00        14.04        16.04        12.99        14.04        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6536 
       11.08        11.01        12.03        20.19        20.42        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.80        16.14        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB 
       12.00        10.26       119.70        49.91         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
        7.76        81.37        60.79        98.24        95.18         8.61 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
       13.64        13.45         6.18        35.87         1.55        29.59 
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-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 
       74.56        67.30        53.62        51.75        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        47.15        52.80        18.18 
TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 
       19.33        31.30        70.03        24.13        10.39        16.83 
TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3612 
       10.39         8.02        20.05        12.03         6.05        19.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       29.98         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
        0.99        20.98        36.03         9.07        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 
       38.96        61.97         1.45         1.81         9.37         4.73 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6681 
       78.12        15.02        12.99        12.00        36.00        12.95 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6883 
       32.61        20.55        19.96        15.85         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 
       13.64        17.46        32.19         0.66         1.12        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                      140.38                       135.65 
  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE 
                        19.0                         19.2 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.2)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   247 113
  DEL PEAK 37(17P12) WILD-TYPE 195  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    247  113
  DEL PEAK 37(17P12) WILD-TYPE  195   49
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  COLON                         247                          195
  RECTUM                        113                           49
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(17P12) MUTATED        53        0       19        87         3
  DEL PEAK 37(17P12) WILD-TYPE      51        1       17        84         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17P12) MUTATED           1        16         16         52
  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           42       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                            53                           51
  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                         52                           27
  STAGE IIIC                         42                           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  61 252  42
  DEL PEAK 37(17P12) WILD-TYPE  11  46 161  24
D64V5, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  T1                          9                           11
  T2                         61                           46
  T3                        252                          161
  T4                         42                           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   177 102  83
  DEL PEAK 37(17P12) WILD-TYPE 165  47  31
D64V6, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  N0                        177                          165
  N1                        102                           47
  N2                         83                           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"
D64V7, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   258  65
  DEL PEAK 37(17P12) WILD-TYPE 190  21
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    258   65
  DEL PEAK 37(17P12) WILD-TYPE  190   21
   clus
vv  DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  0                        258                          190
  1                         65                           21
[1] 2 2
[1] FALSE
D64V8, binary
                              cls
clus                             0   1
  DEL PEAK 37(17P12) MUTATED   167 197
  DEL PEAK 37(17P12) WILD-TYPE 119 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED    167  197
  DEL PEAK 37(17P12) WILD-TYPE  119  125
        clus
vv       DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  FEMALE                        167                          119
  MALE                          197                          125
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                    229
  DEL PEAK 37(17P12) WILD-TYPE                  152
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(17P12) MUTATED                              17
  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                                  229
  COLON MUCINOUS ADENOCARCINOMA                          17
  RECTAL ADENOCARCINOMA                                 105
  RECTAL MUCINOUS ADENOCARCINOMA                          6
                                clus
vv                               DEL PEAK 37(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                    152
  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     7 357
  DEL PEAK 37(17P12) WILD-TYPE   2 242
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 37(17P12) MUTATED      7  357
  DEL PEAK 37(17P12) WILD-TYPE    2  242
     clus
vv    DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  NO                           7                            2
  YES                        357                          242
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 37(17P12) MUTATED   258   3  26  13
  DEL PEAK 37(17P12) WILD-TYPE 181   2  10  16
D64V11, multiclass
    clus
vv   DEL PEAK 37(17P12) MUTATED DEL PEAK 37(17P12) WILD-TYPE
  R0                        258                          181
  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                          35   175
  DEL PEAK 37(17P12) WILD-TYPE                        25   117
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 37(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                35
  WHITE                                                   175
                                  clus
vv                                 DEL PEAK 37(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  25
  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    69  23
  DEL PEAK 38(17Q24.3) WILD-TYPE 399  92
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            92                            491 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                            23                             92 
$`DEL PEAK 38(17Q24.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 
       43.76        43.76        37.05        32.45        31.63        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 
       25.18        24.16        24.03        12.99        21.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 
        6.05         2.01        50.04        37.05        19.00        10.06 
TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3989 
       37.02        31.07        27.02        24.00        26.01         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       34.03        42.02        10.98        32.02        33.04         2.96 
TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D 
       39.98         5.79        22.42         0.20         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4747 
       18.84        12.10         3.29         0.26        49.08        25.02 
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        45.40        43.27 
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        13.25         8.35        10.98         9.93        12.79 
TCGA-QG-A5YV TCGA-QL-A97D TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3581 
       42.77         9.70        14.50        15.39        65.98         7.07 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 
       36.03         1.02         1.02        32.02        28.04        13.94 
TCGA-AG-A00H TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 
       25.97         9.07        12.00        41.00         0.69        10.19 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 
       13.97        15.02        10.98         5.29        24.13        20.91 
TCGA-EI-6881 TCGA-F5-6814 
       16.41         0.53 

$`DEL PEAK 38(17Q24.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.25        37.02        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-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-3522 
        1.02        13.02        38.99         1.02         9.07        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01         0.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-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-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
        5.98        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 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        14.93         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
        0.99        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98         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-A5EK 
       56.55         0.79         0.72        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       15.75        21.44        17.82        17.26        19.33        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         4.80        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        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       65.85        53.62        44.68        55.04        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        18.18        19.33        19.33        15.65 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       13.05        12.00        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       30.28        70.03        24.13        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       13.55        19.10        12.72        37.74        10.39        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
       32.02         8.02        20.05        24.00        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-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-3898 TCGA-AG-3909 
       17.03        13.02        35.01        14.01        48.03        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-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J 
        6.02        23.01        37.02        15.95        36.03         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72        26.43         1.81         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        78.12         7.17        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
       11.01        15.02        12.99        12.00        36.00        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-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-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-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        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19         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 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE 
                         17.13                          19.33 
[1] "0.2 - 140.4 (17.1)" "0.0 - 139.2 (19.3)"
[1] "hr=" "1.5"
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    69  25
  DEL PEAK 38(17Q24.3) WILD-TYPE 373 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     69   25
  DEL PEAK 38(17Q24.3) WILD-TYPE  373  137
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON                            69                            373
  RECTUM                           25                            137
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(17Q24.3) MUTATED        15        0        5        15         0
  DEL PEAK 38(17Q24.3) WILD-TYPE      89        1       31       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         68
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(17Q24.3) MUTATED           15       12         9         1
  DEL PEAK 38(17Q24.3) WILD-TYPE         39       49        18         1
D65V4, multiclass
            clus
vv           DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  STAGE I                              15                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            15                            156
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            5                             16
  STAGE IIIB                           11                             68
  STAGE IIIC                           15                             39
  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  19  62  14
  DEL PEAK 38(17Q24.3) WILD-TYPE  20  88 351  52
D65V5, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  T1                            0                             20
  T2                           19                             88
  T3                           62                            351
  T4                           14                             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 38(17Q24.3) MUTATED    38  30  27
  DEL PEAK 38(17Q24.3) WILD-TYPE 304 119  87
D65V6, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  N0                           38                            304
  N1                           30                            119
  N2                           27                             87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    59  21
  DEL PEAK 38(17Q24.3) WILD-TYPE 389  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     59   21
  DEL PEAK 38(17Q24.3) WILD-TYPE  389   65
   clus
vv  DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  0                           59                            389
  1                           21                             65
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(17Q24.3) MUTATED    39  56
  DEL PEAK 38(17Q24.3) WILD-TYPE 247 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED     39   56
  DEL PEAK 38(17Q24.3) WILD-TYPE  247  266
        clus
vv       DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  FEMALE                           39                            247
  MALE                             56                            266
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                     59
  DEL PEAK 38(17Q24.3) WILD-TYPE                  322
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17Q24.3) MUTATED                              10
  DEL PEAK 38(17Q24.3) WILD-TYPE                            50
                                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                                     59
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    22
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 38(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      322
  COLON MUCINOUS ADENOCARCINOMA                              50
  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  93
  DEL PEAK 38(17Q24.3) WILD-TYPE   7 506
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(17Q24.3) MUTATED      2   93
  DEL PEAK 38(17Q24.3) WILD-TYPE    7  506
     clus
vv    DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  NO                             2                              7
  YES                           93                            506
[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 376   5  28  23
D65V11, multiclass
    clus
vv   DEL PEAK 38(17Q24.3) MUTATED DEL PEAK 38(17Q24.3) WILD-TYPE
  R0                           63                            376
  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                          10    45
  DEL PEAK 38(17Q24.3) WILD-TYPE                        50   247
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 38(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 38(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    50
  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   287  63
  DEL PEAK 39(18P11.31) WILD-TYPE 181  52
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                            350                             233 
  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE 
                             63                              52 
$`DEL PEAK 39(18P11.31) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       16.57        37.05        37.25        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       32.71        29.16        27.09        24.13        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 
        1.02         6.97        38.99         9.07        37.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
       19.07        34.03        29.00        26.01        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-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-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 
       15.02        37.05        19.00        36.00        85.05        25.02 
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        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       33.07         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-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-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       24.00         7.96        13.94        19.00        34.03        38.04 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        14.99        21.99        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       32.02        31.00         1.02        33.04        26.01         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
       39.98         2.01         5.03        41.00        40.96         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         5.79        22.42        27.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50         0.95        15.75        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         5.65         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
       62.79        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-5912 
        2.14         3.29         0.07         0.26         1.35        49.08 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       21.99         2.01        25.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       13.51        11.51        20.19        18.25         1.32        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       17.13        12.49         7.53        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       13.41        11.38        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E 
       12.59       140.38        44.32       139.17        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
       35.97       117.07        95.18        13.38        11.11        13.45 
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        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
        0.53        35.41        28.21         8.35        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       65.85        55.04        45.11        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC 
       46.75        47.15        18.18        10.98        19.33        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       13.05        12.00        42.77        32.98         8.42         9.70 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       30.28        24.13        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56K 
       12.72        37.74        10.39        14.50        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       65.98        11.84        36.03         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
       24.00        46.03        34.03        50.04         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99        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-4007 
       48.03        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       17.03         0.99        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       10.98        51.98         1.94        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        26.43        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        78.12         7.17 
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        10.98        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-6509 TCGA-EI-6510 
       51.48         0.49         2.40        20.55        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       10.78        13.64        11.97        37.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39        32.19         0.66         0.69         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 
       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        42.90        37.02        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-3529 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
        0.00        29.00        12.99         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       29.95        20.98        61.02         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       47.05        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       24.00         2.01         2.01        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       27.02        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
        0.99        17.03        34.98        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07         1.02        35.01        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
       21.37        56.55         0.72        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X 
       27.09        16.31         0.20        21.44        17.82        19.33 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 
       50.37        58.39         1.41        32.94        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         3.19         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        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-4751 TCGA-CM-5348 TCGA-CM-5860 
       20.02        37.02        26.04        27.02        22.98        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 
       14.04        12.95        13.05        11.08        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       17.75        43.27        15.12         4.80        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        10.13         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA 
       10.26       119.70        92.75        49.91         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G 
      135.65         7.76         6.12        14.04        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 
       98.24         8.61        13.64         6.18        35.87        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
      107.67        74.56        67.30        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-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       35.80        26.17        52.80        19.33         9.93        15.65 
TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 
       29.46        31.30        70.03        19.10        16.83        15.39 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-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                            0.00 
  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 
                          19.00                           19.33 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.3)"
[1] "hr=" "1.2"
D66V2, continuous
D66V3, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   240 122
  DEL PEAK 39(18P11.31) WILD-TYPE 202  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    240  122
  DEL PEAK 39(18P11.31) WILD-TYPE  202   40
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  COLON                            240                             202
  RECTUM                           122                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18P11.31) MUTATED        57        0       14        96         4
  DEL PEAK 39(18P11.31) WILD-TYPE      47        1       22        75         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18P11.31) MUTATED           3        12         13         52
  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         20       14         3         1
D66V4, multiclass
            clus
vv           DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  STAGE I                               57                              47
  STAGE IA                               0                               1
  STAGE II                              14                              22
  STAGE IIA                             96                              75
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             12                              14
  STAGE IIIA                            13                               8
  STAGE IIIB                            52                              27
  STAGE IIIC                            34                              20
  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  62 251  41
  DEL PEAK 39(18P11.31) WILD-TYPE   9  45 162  25
D66V5, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  T1                            11                               9
  T2                            62                              45
  T3                           251                             162
  T4                            41                              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   187 103  73
  DEL PEAK 39(18P11.31) WILD-TYPE 155  46  41
D66V6, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  N0                           187                             155
  N1                           103                              46
  N2                            73                              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   254  71
  DEL PEAK 39(18P11.31) WILD-TYPE 194  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    254   71
  DEL PEAK 39(18P11.31) WILD-TYPE  194   15
   clus
vv  DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  0                           254                             194
  1                            71                              15
[1] 2 2
[1] FALSE
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 39(18P11.31) MUTATED   169 196
  DEL PEAK 39(18P11.31) WILD-TYPE 117 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED    169  196
  DEL PEAK 39(18P11.31) WILD-TYPE  117  126
        clus
vv       DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  FEMALE                           169                             117
  MALE                             196                             126
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                    229
  DEL PEAK 39(18P11.31) WILD-TYPE                  152
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(18P11.31) MUTATED                              10
  DEL PEAK 39(18P11.31) WILD-TYPE                            50
                                 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                                     229
  COLON MUCINOUS ADENOCARCINOMA                             10
  RECTAL ADENOCARCINOMA                                    116
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 39(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       152
  COLON MUCINOUS ADENOCARCINOMA                               50
  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     7 358
  DEL PEAK 39(18P11.31) WILD-TYPE   2 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 39(18P11.31) MUTATED      7  358
  DEL PEAK 39(18P11.31) WILD-TYPE    2  241
     clus
vv    DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  NO                              7                               2
  YES                           358                             241
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 39(18P11.31) MUTATED   260   2  29  14
  DEL PEAK 39(18P11.31) WILD-TYPE 179   3   7  15
D66V11, multiclass
    clus
vv   DEL PEAK 39(18P11.31) MUTATED DEL PEAK 39(18P11.31) WILD-TYPE
  R0                           260                             179
  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                          38   180
  DEL PEAK 39(18P11.31) WILD-TYPE                        22   112
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 39(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      180
                                  clus
vv                                 DEL PEAK 39(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     22
  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   318  74
  DEL PEAK 40(18Q12.2) WILD-TYPE 150  41
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                           392                            191 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                            74                             41 
$`DEL PEAK 40(18Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        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 
       16.57        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02         6.97        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       36.03        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-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-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 
        5.98        37.05        19.00        36.00        85.05        25.02 
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        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       33.07         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 
       27.02        29.98        18.05        12.99        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       34.06        26.01        24.00        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        18.05        42.02        17.03        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S 
       15.02        15.02        10.98        32.02        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       33.04        26.01        37.02         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 
        5.03         0.92        41.00        40.96         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        5.79        22.42        27.42        10.88         0.20        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.46        14.50        16.31        15.75        17.26        17.85 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84        75.25         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
       62.79        61.41        12.10        29.56         5.23         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
      102.44        49.08        21.99         2.01        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
       27.02        13.02        29.06        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        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        45.40        12.26        19.59        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-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       131.51       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      119.93       117.07        95.18         8.61        13.38        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       13.45         1.55        16.31        29.59        16.24        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
        0.53        35.41        28.21         8.35        82.39        23.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       65.85        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.72        36.00        91.79        46.75        47.15        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.98        19.33        12.79        13.05        12.00        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 
       32.98         8.42         9.70        30.28        24.13        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        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-3587 TCGA-AG-3593 TCGA-AG-3594 
       36.03        20.05        24.00        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       50.04         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        0.99        29.98         1.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        36.95        17.03        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        51.98         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       38.04         0.49         0.69         0.72        26.43        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 
       78.12         7.17        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        10.98        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        37.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK 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        42.90        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-3529 TCGA-AA-3534 
        1.02        13.02         1.02         8.05         0.00        29.00 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 
        0.99        17.95        29.95        20.98         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        0.92        47.05        11.01         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04        10.06        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95         0.00         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
        2.01        25.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        38.04         4.01        27.02         0.99 
TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       34.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       35.01        39.06        51.98        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AM-5821 TCGA-AU-6004 
        0.07        21.37        56.55         0.72         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 
        0.95         0.20        21.44        17.82        19.33        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 
       58.39         1.41         5.65        32.94        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
      100.01        11.74         3.19         3.06         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        14.99        12.99        14.04        12.95        13.05 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        15.12         4.80        16.14 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.39         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      119.70       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        13.64         6.18        35.87        33.67        19.43 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      107.67        74.56        67.30        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       19.33         9.93        15.65        29.46        31.30        70.03 
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
       16.83         8.02         1.02        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A025 
       13.02        14.01        20.98        36.03         9.07        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE 
                         19.00                          19.33 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.3)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   268 139
  DEL PEAK 40(18Q12.2) WILD-TYPE 174  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    268  139
  DEL PEAK 40(18Q12.2) WILD-TYPE  174   23
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON                           268                            174
  RECTUM                          139                             23
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18Q12.2) MUTATED        60        0       21       105         4
  DEL PEAK 40(18Q12.2) WILD-TYPE      44        1       15        66         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q12.2) MUTATED           3        15         17         59
  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         14        9         4         1
D67V4, multiclass
            clus
vv           DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  STAGE I                              60                             44
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                           105                             66
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            15                             11
  STAGE IIIA                           17                              4
  STAGE IIIB                           59                             20
  STAGE IIIC                           40                             14
  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  68 287  43
  DEL PEAK 40(18Q12.2) WILD-TYPE   9  39 126  23
D67V5, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  T1                           11                              9
  T2                           68                             39
  T3                          287                            126
  T4                           43                             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   205 115  87
  DEL PEAK 40(18Q12.2) WILD-TYPE 137  34  27
D67V6, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  N0                          205                            137
  N1                          115                             34
  N2                           87                             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"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   292  73
  DEL PEAK 40(18Q12.2) WILD-TYPE 156  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    292   73
  DEL PEAK 40(18Q12.2) WILD-TYPE  156   13
   clus
vv  DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  0                          292                            156
  1                           73                             13
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q12.2) MUTATED   186 224
  DEL PEAK 40(18Q12.2) WILD-TYPE 100  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED    186  224
  DEL PEAK 40(18Q12.2) WILD-TYPE  100   98
        clus
vv       DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  FEMALE                          186                            100
  MALE                            224                             98
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                    252
  DEL PEAK 40(18Q12.2) WILD-TYPE                  129
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18Q12.2) MUTATED                              15
  DEL PEAK 40(18Q12.2) WILD-TYPE                            45
                                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                                    252
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                   128
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 40(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      129
  COLON MUCINOUS ADENOCARCINOMA                              45
  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     9 401
  DEL PEAK 40(18Q12.2) WILD-TYPE   0 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q12.2) MUTATED      9  401
  DEL PEAK 40(18Q12.2) WILD-TYPE    0  198
     clus
vv    DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  NO                             9                              0
  YES                          401                            198
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(18Q12.2) MUTATED   293   3  29  14
  DEL PEAK 40(18Q12.2) WILD-TYPE 146   2   7  15
D67V11, multiclass
    clus
vv   DEL PEAK 40(18Q12.2) MUTATED DEL PEAK 40(18Q12.2) WILD-TYPE
  R0                          293                            146
  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                          38   203
  DEL PEAK 40(18Q12.2) WILD-TYPE                        22    89
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  38
  WHITE                                                     203
                                  clus
vv                                 DEL PEAK 40(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    22
  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  78
  DEL PEAK 41(18Q21.2) WILD-TYPE 137  37
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                           409                            174 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                            78                             37 
$`DEL PEAK 41(18Q21.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        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 
       16.57        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       24.13        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3860 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-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-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q 
       27.02         7.96        19.00        34.03        18.05        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        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       32.02        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96         4.21         0.79         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
        0.20        16.44         0.46        14.50        16.31        15.75 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       17.82        17.26        17.85        18.84        75.25         5.65 
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-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-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
      102.44        49.08        21.99         2.01        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
       27.02        13.02        29.06        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        11.01        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        17.75        18.25         1.32 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85        17.13        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
       14.04        26.47       119.93        35.97       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 
       95.18         8.61        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        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       35.41        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       65.85        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       36.72        36.00        26.04        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 
       18.18        10.98        19.33         9.93        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       12.00        42.77        32.98         8.42         9.70        30.28 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        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-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 
       36.03        14.04         1.02        17.03         0.99        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-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        26.43        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        78.12         7.17 
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        10.98        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-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        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       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        42.90        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-3529 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 
        1.02         8.05         0.00        29.00         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       29.95        20.98         6.97         0.92        47.05        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
        0.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00        36.03        32.05        53.00        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 
       33.01        26.01        24.00         2.01        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L 
       27.02        13.94        38.04        30.02        18.05        38.04 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I 
        4.01        27.02         0.99        34.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
       38.07         1.02        35.01        35.01        39.06        51.98 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 
        0.72        10.88         0.92        27.09         0.95         0.20 
TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       21.44        19.33        50.37        58.39         1.41        32.94 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       49.41         6.77       100.01         3.06         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6530 
       12.00        14.99        12.99        14.04        12.95        20.42 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       43.27        15.12         4.80        16.14        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64         1.51        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       19.43       107.67        67.30        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       22.09        13.78        35.80        26.17        52.80        19.33 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3580 
       15.65        29.46        31.30        70.03        16.83         8.02 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       12.03        19.99         0.99        13.02        14.01        20.98 
TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DY-A1H8 
       36.03        49.97        61.97         1.45         1.81        32.61 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       19.96         8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE 
                         19.00                          19.38 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.4)"
[1] "hr=" "1.1"
D68V2, continuous
D68V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   282 142
  DEL PEAK 41(18Q21.2) WILD-TYPE 160  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    282  142
  DEL PEAK 41(18Q21.2) WILD-TYPE  160   20
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON                           282                            160
  RECTUM                          142                             20
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(18Q21.2) MUTATED        62        0       23       107         4
  DEL PEAK 41(18Q21.2) WILD-TYPE      42        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q21.2) MUTATED           3        16         17         62
  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         11        6         3         0
D68V4, multiclass
            clus
vv           DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           107                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           17                              4
  STAGE IIIB                           62                             17
  STAGE IIIC                           43                             11
  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  69 298  47
  DEL PEAK 41(18Q21.2) WILD-TYPE   8  38 115  19
D68V5, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  T1                           12                              8
  T2                           69                             38
  T3                          298                            115
  T4                           47                             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   211 119  94
  DEL PEAK 41(18Q21.2) WILD-TYPE 131  30  20
D68V6, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  N0                          211                            131
  N1                          119                             30
  N2                           94                             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"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   302  78
  DEL PEAK 41(18Q21.2) WILD-TYPE 146   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    302   78
  DEL PEAK 41(18Q21.2) WILD-TYPE  146    8
   clus
vv  DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  0                          302                            146
  1                           78                              8
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q21.2) MUTATED   191 236
  DEL PEAK 41(18Q21.2) WILD-TYPE  95  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED    191  236
  DEL PEAK 41(18Q21.2) WILD-TYPE   95   86
        clus
vv       DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  FEMALE                          191                             95
  MALE                            236                             86
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                    264
  DEL PEAK 41(18Q21.2) WILD-TYPE                  117
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q21.2) MUTATED                              17
  DEL PEAK 41(18Q21.2) WILD-TYPE                            43
                                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                                    264
  COLON MUCINOUS ADENOCARCINOMA                            17
  RECTAL ADENOCARCINOMA                                   129
  RECTAL MUCINOUS ADENOCARCINOMA                           11
                                clus
vv                               DEL PEAK 41(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      117
  COLON MUCINOUS ADENOCARCINOMA                              43
  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     9 418
  DEL PEAK 41(18Q21.2) WILD-TYPE   0 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q21.2) MUTATED      9  418
  DEL PEAK 41(18Q21.2) WILD-TYPE    0  181
     clus
vv    DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  NO                             9                              0
  YES                          418                            181
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(18Q21.2) MUTATED   303   3  30  15
  DEL PEAK 41(18Q21.2) WILD-TYPE 136   2   6  14
D68V11, multiclass
    clus
vv   DEL PEAK 41(18Q21.2) MUTATED DEL PEAK 41(18Q21.2) WILD-TYPE
  R0                          303                            136
  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                          42   212
  DEL PEAK 41(18Q21.2) WILD-TYPE                        18    80
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  42
  WHITE                                                     212
                                  clus
vv                                 DEL PEAK 41(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    18
  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  78
  DEL PEAK 42(18Q22.1) WILD-TYPE 141  37
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                           405                            178 
  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE 
                            78                             37 
$`DEL PEAK 42(18Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       11.47         4.80        11.47        43.76        43.76        43.43 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       24.33        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 
       16.57        37.05        37.25        37.02        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       24.13        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05         1.02         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        23.01        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       50.04        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03        10.06        33.07         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-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       18.05        12.99        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       24.00        27.02         7.96        13.94        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
       10.98        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        40.96         4.21         0.79         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42         0.20        16.44         0.46        14.50        16.31 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       15.75        17.26        17.85        18.84        75.25         5.65 
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-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-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        2.24         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       49.08        21.99         2.01        25.02         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        45.40        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       11.51        20.19        17.75        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.85        17.13        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50        44.32       131.51       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
       14.04        26.47       119.93        35.97       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 
       95.18         8.61        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        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       35.41        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       65.85        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.72        36.00        91.79        46.75        47.15        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        19.33         9.93        12.79        13.05        12.00 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       42.77        32.98         8.42         9.70        30.28        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
        7.07        36.03        20.05        24.00        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-3732 TCGA-AG-3742 TCGA-AG-3882 
        7.99         0.99        29.98        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        36.95        17.03        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        15.95         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         0.49         0.69         0.72        26.43 
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        78.12         7.17        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        10.98 
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-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         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-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        37.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       32.19         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        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        42.90        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-3529 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 
        1.02         8.05         0.00        29.00         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       29.95        20.98         6.97         0.92        47.05        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04        19.04        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
        0.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
        0.00        36.03        32.05        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-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        38.04         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-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       10.88         0.92        27.09         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.82        19.33        50.37        58.39         1.41        32.94 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
       49.41         6.77       100.01         3.06         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-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-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 
       20.42        43.27         4.80        16.14        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB 
       11.64         1.51        12.00        10.26       119.70       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
        7.76        81.37        60.79        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
       19.43       107.67        67.30        53.62        51.75        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       22.09        26.04        13.78        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 
       19.33        15.65        29.46        31.30        70.03        16.83 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 
        8.02         1.02        12.03        19.99         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                           0.00 
  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 
                         19.00                          19.33 
[1] "0.1 - 140.4 (19.0)" "0.0 - 135.7 (19.3)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   281 138
  DEL PEAK 42(18Q22.1) WILD-TYPE 161  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    281  138
  DEL PEAK 42(18Q22.1) WILD-TYPE  161   24
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON                           281                            161
  RECTUM                          138                             24
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(18Q22.1) MUTATED        62        0       23       107         4
  DEL PEAK 42(18Q22.1) WILD-TYPE      42        1       13        64         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q22.1) MUTATED           3        14         16         61
  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         11        7         3         0
D69V4, multiclass
            clus
vv           DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           107                             64
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            14                             12
  STAGE IIIA                           16                              5
  STAGE IIIB                           61                             18
  STAGE IIIC                           43                             11
  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  69 293  47
  DEL PEAK 42(18Q22.1) WILD-TYPE   8  38 120  19
D69V5, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  T1                           12                              8
  T2                           69                             38
  T3                          293                            120
  T4                           47                             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   211 115  93
  DEL PEAK 42(18Q22.1) WILD-TYPE 131  34  21
D69V6, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  N0                          211                            131
  N1                          115                             34
  N2                           93                             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"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   299  77
  DEL PEAK 42(18Q22.1) WILD-TYPE 149   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    299   77
  DEL PEAK 42(18Q22.1) WILD-TYPE  149    9
   clus
vv  DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  0                          299                            149
  1                           77                              9
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q22.1) MUTATED   189 233
  DEL PEAK 42(18Q22.1) WILD-TYPE  97  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED    189  233
  DEL PEAK 42(18Q22.1) WILD-TYPE   97   89
        clus
vv       DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  FEMALE                          189                             97
  MALE                            233                             89
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                    264
  DEL PEAK 42(18Q22.1) WILD-TYPE                  117
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q22.1) MUTATED                              16
  DEL PEAK 42(18Q22.1) WILD-TYPE                            44
                                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                                    264
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                   127
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 42(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      117
  COLON MUCINOUS ADENOCARCINOMA                              44
  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     9 413
  DEL PEAK 42(18Q22.1) WILD-TYPE   0 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q22.1) MUTATED      9  413
  DEL PEAK 42(18Q22.1) WILD-TYPE    0  186
     clus
vv    DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  NO                             9                              0
  YES                          413                            186
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q22.1) MUTATED   300   3  29  15
  DEL PEAK 42(18Q22.1) WILD-TYPE 139   2   7  14
D69V11, multiclass
    clus
vv   DEL PEAK 42(18Q22.1) MUTATED DEL PEAK 42(18Q22.1) WILD-TYPE
  R0                          300                            139
  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                          41   210
  DEL PEAK 42(18Q22.1) WILD-TYPE                        19    82
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  41
  WHITE                                                     210
                                  clus
vv                                 DEL PEAK 42(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    19
  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  24
  DEL PEAK 43(19P13.3) WILD-TYPE 402  91
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            90                            493 
  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE 
                            24                             91 
$`DEL PEAK 43(19P13.3) MUTATED`
TCGA-4N-A93T TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3506 
        4.80        34.65        25.08        21.76        61.84        58.03 
TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 
        9.07        26.01        12.99        13.02        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3850 
        6.05         2.01        36.00        36.95        37.02         0.00 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3952 
       31.07        17.03        24.03        27.02        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T 
       50.99        24.00        27.02        10.98        12.00        33.04 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 
       26.01        39.98        41.00        22.42         0.20        16.31 
TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 
        0.20         5.13        65.00         3.29       102.44        49.08 
TCGA-CM-6169 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 
       13.02        13.05        10.06        45.40        20.19         1.32 
TCGA-D5-6537 TCGA-D5-6541 TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA 
        4.80        15.58        10.13       119.70        44.32       131.51 
TCGA-F4-6461 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U 
       11.11        33.67         8.35        82.39        36.00        10.98 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 
       30.28        24.13        39.48        14.50        12.00        36.03 
TCGA-AG-3608 TCGA-AG-3732 TCGA-AG-3893 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 
       15.95        32.98        35.01        17.03        15.95         9.07 
TCGA-AG-A01Y TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-4957 TCGA-DC-5869 TCGA-DC-6155 
       64.01         6.05         6.05        13.97        12.99        13.97 
TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 
       10.98         5.29       129.27        24.13        51.48        17.00 
TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 
       16.34        13.64        31.30        28.57         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 
       11.47        11.47        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       42.90        24.33        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        16.57        37.05        37.25        37.02        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        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 
       24.03        37.05        36.03         8.05        19.07         0.00 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-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-3696 TCGA-AA-3697 
       11.01         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        19.04        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        12.99        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        25.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        38.04         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-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-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
        1.02        35.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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         5.79        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10         1.35        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         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        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5538 
       12.95        11.08        11.08        11.01        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        13.51        11.51        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38         7.50       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        13.25         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        23.51        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       13.05        12.00        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       31.30         9.70        70.03        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        16.83        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        20.05        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        26.43 
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        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
        7.17        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        32.19         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                              0 
  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 
                         20.09                          19.07 
[1] "0.0 - 131.5 (20.1)" "0.0 - 140.4 (19.1)"
[1] "hr=" "1.3"
D70V2, continuous
D70V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    62  33
  DEL PEAK 43(19P13.3) WILD-TYPE 380 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     62   33
  DEL PEAK 43(19P13.3) WILD-TYPE  380  129
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  COLON                            62                            380
  RECTUM                           33                            129
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(19P13.3) MUTATED        11        0        4        19         0
  DEL PEAK 43(19P13.3) WILD-TYPE      93        1       32       152        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(19P13.3) MUTATED           1         5          5         10
  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         39       46        19         1
D70V4, multiclass
            clus
vv           DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  STAGE I                              11                             93
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            19                            152
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             5                             21
  STAGE IIIA                            5                             16
  STAGE IIIB                           10                             69
  STAGE IIIC                           15                             39
  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  11
  DEL PEAK 43(19P13.3) WILD-TYPE  19  94 342  55
D70V5, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  T1                            1                             19
  T2                           13                             94
  T3                           71                            342
  T4                           11                             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    36  28  32
  DEL PEAK 43(19P13.3) WILD-TYPE 306 121  82
D70V6, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  N0                           36                            306
  N1                           28                            121
  N2                           32                             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"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    63  23
  DEL PEAK 43(19P13.3) WILD-TYPE 385  63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     63   23
  DEL PEAK 43(19P13.3) WILD-TYPE  385   63
   clus
vv  DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  0                           63                            385
  1                           23                             63
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED    40  56
  DEL PEAK 43(19P13.3) WILD-TYPE 246 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED     40   56
  DEL PEAK 43(19P13.3) WILD-TYPE  246  266
        clus
vv       DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  FEMALE                           40                            246
  MALE                             56                            266
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                     56
  DEL PEAK 43(19P13.3) WILD-TYPE                  325
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                               5
  DEL PEAK 43(19P13.3) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                      31
  DEL PEAK 43(19P13.3) WILD-TYPE                   115
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(19P13.3) MUTATED                                1
  DEL PEAK 43(19P13.3) WILD-TYPE                             12
D70V9, multiclass
                                clus
vv                               DEL PEAK 43(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                     56
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 43(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      325
  COLON MUCINOUS ADENOCARCINOMA                              55
  RECTAL ADENOCARCINOMA                                     115
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 43(19P13.3) MUTATED     2  94
  DEL PEAK 43(19P13.3) WILD-TYPE   7 505
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(19P13.3) MUTATED      2   94
  DEL PEAK 43(19P13.3) WILD-TYPE    7  505
     clus
vv    DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  NO                             2                              7
  YES                           94                            505
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(19P13.3) MUTATED    63   1  10   4
  DEL PEAK 43(19P13.3) WILD-TYPE 376   4  26  25
D70V11, multiclass
    clus
vv   DEL PEAK 43(19P13.3) MUTATED DEL PEAK 43(19P13.3) WILD-TYPE
  R0                           63                            376
  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                           8    42
  DEL PEAK 43(19P13.3) WILD-TYPE                        52   250
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 43(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 43(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    52
  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 367  87
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           129                            454 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                            28                             87 
$`DEL PEAK 44(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       24.33        14.53        29.19        23.61        32.71        29.16 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3519 
       24.13        25.18        21.76         1.02        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3561 
       34.03        26.01        12.99         0.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3855 
       78.08         5.98        85.05        25.02        36.95        32.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
       24.03         2.01        20.98         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F 
       42.02        32.02        31.00         1.02        37.02        39.98 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 
       40.96         0.20        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        43.27        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 
       13.25         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 
       19.33        12.00         8.42        30.28        39.48        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        20.05        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        10.98        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 
       28.57         0.46        26.43 

$`DEL PEAK 44(20P12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       11.47         4.80        11.47        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        42.90        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        30.44        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        22.52         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
        0.00        19.07        29.00        29.00        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        13.02        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04        19.04        10.06        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03         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-3956 TCGA-AA-3968 
       24.00        33.01        26.01        24.00        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-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        38.04         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       35.01         1.02        33.04        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         5.79        22.42        27.42 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84        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        49.08        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        25.02 
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        45.40        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         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 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        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        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        18.18 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        19.33         9.93        15.65        12.79        13.05 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       42.77        29.46        32.98        31.30         9.70        70.03 
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-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       37.74        16.83        15.39        20.02        10.39        12.00 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        8.02        36.03         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       50.04        12.03         0.99        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02        32.98         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-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-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 
       61.97        41.00        38.04         0.49         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        78.12         7.17        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.99        13.97        15.02        36.00        12.95        13.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
        5.29       126.44       129.27        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
        8.61        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                         21.99                          18.92 
[1] "0.2 - 131.5 (22.0)" "0.0 - 140.4 (18.9)"
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    83  48
  DEL PEAK 44(20P12.1) WILD-TYPE 359 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     83   48
  DEL PEAK 44(20P12.1) WILD-TYPE  359  114
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  COLON                            83                            359
  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      87        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         58
                                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         38       47        19         2
D71V4, multiclass
            clus
vv           DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  STAGE I                              17                             87
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            31                            140
  STAGE IIB                             0                             10
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            6                             15
  STAGE IIIB                           21                             58
  STAGE IIIC                           16                             38
  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  87 318  52
D71V5, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  T1                            3                             17
  T2                           20                             87
  T3                           95                            318
  T4                           14                             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 44(20P12.1) MUTATED    66  36  30
  DEL PEAK 44(20P12.1) WILD-TYPE 276 113  84
D71V6, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  N0                           66                            276
  N1                           36                            113
  N2                           30                             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED   100  20
  DEL PEAK 44(20P12.1) WILD-TYPE 348  66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED    100   20
  DEL PEAK 44(20P12.1) WILD-TYPE  348   66
   clus
vv  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  0                          100                            348
  1                           20                             66
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    65  67
  DEL PEAK 44(20P12.1) WILD-TYPE 221 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     65   67
  DEL PEAK 44(20P12.1) WILD-TYPE  221  255
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  FEMALE                           65                            221
  MALE                             67                            255
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                     77
  DEL PEAK 44(20P12.1) WILD-TYPE                  304
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(20P12.1) MUTATED                               6
  DEL PEAK 44(20P12.1) WILD-TYPE                            54
                                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                                      304
  COLON MUCINOUS ADENOCARCINOMA                              54
  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   9 467
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED      0  132
  DEL PEAK 44(20P12.1) WILD-TYPE    9  467
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  NO                             0                              9
  YES                          132                            467
[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 348   4  28  26
D71V11, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  R0                           91                            348
  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                        47   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                                    47
  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   159  41
  DEL PEAK 45(21Q11.2) WILD-TYPE 309  74
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           200                            383 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                            41                             74 
$`DEL PEAK 45(21Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 
       43.76        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        10.06        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       10.06         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        38.04        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 
       10.98        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        22.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4616 
       14.50        16.31         0.95        17.85        19.33         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       65.00        12.10        29.56         5.23         3.19         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        2.14         3.29         0.26        49.08        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 
       20.02         8.02        27.02        13.02        22.03        16.01 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 
        5.03        15.02        14.04        29.03        15.02        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 
       11.01        45.40        17.75         1.32        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 
       14.30         9.04        13.41        11.38        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 
      140.38         7.50       131.51        26.47        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
        1.55        29.59        16.24        33.67         0.53        35.41 
TCGA-G4-6295 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 
        8.35        35.93        36.72        36.00        26.43        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-AF-2687 
       46.75        18.18         9.93        13.05        42.77        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       39.48        17.23        19.10        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       10.39        86.63        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3609 
       36.03        24.00        46.03        34.03        12.03        19.99 
TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       29.98        19.99        17.03         1.02        48.03        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03        14.04        17.03        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98         1.94        38.96        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 
        0.49         0.69         4.73        13.97        10.98        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD 
       36.00        10.98        13.05        10.06       126.44        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 
       15.85        17.69        16.34        16.41        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
       31.30         0.39        32.19         0.66         0.53         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 45(21Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       11.47         4.80        11.47        46.65        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       24.33        44.91        35.11        45.60        13.94        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 
       31.63        29.19        33.53        23.61        32.71        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-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.69        20.12        19.66        16.24        24.92        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        7.04         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 
       58.03        63.98         1.02        13.02         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       37.05        36.03         8.05         0.00        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        33.99        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       29.95        20.98        13.94        19.99        61.02         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-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       31.07        53.00        29.98        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00         2.01        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       14.99        34.98        15.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06         2.96         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         5.79        27.42        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        15.75         0.20        21.44        17.82        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       18.84        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-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         1.94         3.06         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-5913 TCGA-CK-5916 TCGA-CK-6747 
       40.34        70.16        15.62        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 
      124.27        23.05        37.02        25.02        26.04        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        12.26        19.59        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        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DB 
       24.43        38.20       130.65        92.75        12.59        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        13.64        13.45         6.18        16.31 
TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       13.25        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       51.75        45.11        39.42        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       35.80        26.17        47.15        52.80        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        15.65        12.79        12.00        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2691 
        8.42        31.30         9.70        30.28        70.03        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-A56L 
       13.55        12.72        37.74        10.39        16.83        65.98 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       32.02         8.02        20.05         1.02         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-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 
       13.02        35.01        14.01        32.02        28.04         1.02 
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-A023 
       37.02        15.95        36.03         9.07         1.02        51.98 
TCGA-AG-A025 TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        38.04         1.45         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       10.19         6.05         6.05         6.97         9.37        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        7.17        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
       30.05        12.95         5.29        41.36       129.27        24.13 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       19.96        17.00        18.28        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       10.78        13.64        17.46         9.96        37.51        28.57 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.46        55.76        47.08 

  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                         18.64                          19.33 
[1] "0.2 - 140.4 (18.6)" "0.0 - 139.2 (19.3)"
[1] "hr=" "1.2"
D72V2, continuous
D72V3, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   136  71
  DEL PEAK 45(21Q11.2) WILD-TYPE 306  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    136   71
  DEL PEAK 45(21Q11.2) WILD-TYPE  306   91
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON                           136                            306
  RECTUM                           71                             91
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 45(21Q11.2) MUTATED        34        0       14        53         2
  DEL PEAK 45(21Q11.2) WILD-TYPE      70        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         52
                                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         33       33        20         2
D72V4, multiclass
            clus
vv           DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  STAGE I                              34                             70
  STAGE IA                              0                              1
  STAGE II                             14                             22
  STAGE IIA                            53                            118
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                           11                             10
  STAGE IIIB                           27                             52
  STAGE IIIC                           21                             33
  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  40 140  23
  DEL PEAK 45(21Q11.2) WILD-TYPE  13  67 273  43
D72V5, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  T1                            7                             13
  T2                           40                             67
  T3                          140                            273
  T4                           23                             43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 45(21Q11.2) MUTATED   106  56  48
  DEL PEAK 45(21Q11.2) WILD-TYPE 236  93  66
D72V6, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  N0                          106                            236
  N1                           56                             93
  N2                           48                             66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   150  33
  DEL PEAK 45(21Q11.2) WILD-TYPE 298  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    150   33
  DEL PEAK 45(21Q11.2) WILD-TYPE  298   53
   clus
vv  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  0                          150                            298
  1                           33                             53
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    96 114
  DEL PEAK 45(21Q11.2) WILD-TYPE 190 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     96  114
  DEL PEAK 45(21Q11.2) WILD-TYPE  190  208
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  FEMALE                           96                            190
  MALE                            114                            208
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                    127
  DEL PEAK 45(21Q11.2) WILD-TYPE                  254
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                               8
  DEL PEAK 45(21Q11.2) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                      66
  DEL PEAK 45(21Q11.2) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                3
  DEL PEAK 45(21Q11.2) WILD-TYPE                             10
D72V9, multiclass
                                clus
vv                               DEL PEAK 45(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    127
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      254
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED     5 205
  DEL PEAK 45(21Q11.2) WILD-TYPE   4 394
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED      5  205
  DEL PEAK 45(21Q11.2) WILD-TYPE    4  394
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  NO                             5                              4
  YES                          205                            394
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(21Q11.2) MUTATED   149   2  14   7
  DEL PEAK 45(21Q11.2) WILD-TYPE 290   3  22  22
D72V11, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  R0                          149                            290
  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                          18   105
  DEL PEAK 45(21Q11.2) WILD-TYPE                        42   187
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     105
                                  clus
vv                                 DEL PEAK 45(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    42
  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   164  48
  DEL PEAK 46(22Q13.32) WILD-TYPE 304  67
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            212                             371 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                             48                              67 
$`DEL PEAK 46(22Q13.32) MUTATED`
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
        4.80        43.76        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 
       13.94        16.57        34.65        36.53        14.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 
       30.44        29.19        23.61        22.52        20.61        21.76 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 
       23.87        61.84        56.25         9.63         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        9.07        24.03        37.05        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 
       33.99        21.01        13.02        19.99        13.94         6.05 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
        2.01        50.04         5.98        37.05        85.05        10.06 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 
       27.02        29.98        18.05         2.01        12.99         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 
        2.01        21.99        50.99        13.05        26.01         7.96 
TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       13.94        34.03        27.02        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F 
       21.99        15.02        33.04        26.01        37.02        39.98 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00        40.96         5.79        22.42         0.20        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 
       14.50        16.31        15.75         0.20        17.85         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.65         5.13        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 
        1.94         2.24         3.06         0.26         1.35        49.08 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 
        2.01        25.02         8.02        29.06        30.08         5.03 
TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       15.02        15.02        11.08        11.01        10.06        45.40 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       13.51        20.19         1.32        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
       12.49         7.53        12.43        13.41        11.38       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       13.32        12.59       140.38        44.32       131.51         6.12 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 
       26.47        13.38         1.55        16.24        13.25         8.35 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       82.39        51.75        45.11        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        18.18        10.98        19.33         9.93        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       29.46         9.70        30.28        13.55        19.10        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       15.39        10.39        65.98        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 
       36.03        20.05        24.00        34.03        50.04        15.95 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 
       29.98         1.02        19.99         1.02         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03        14.04        25.97        23.01        12.00 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 
       10.98         1.94        38.96        41.00         0.49         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
       10.19         6.05         4.73        13.97        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97        10.98        30.05        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 
       41.36        51.48        32.61         2.40        20.55        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 
       16.31        16.41        28.57         0.39         0.66         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       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 
       11.47        11.47        46.65        43.76        43.43        42.90 
TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       24.33        37.05        37.25        37.02        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         7.04         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       29.00         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       23.01        20.98        19.99        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       15.95        14.93         0.00         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       20.98        34.03        16.08        34.06        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-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05        38.04         4.01         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A024 
       38.07         1.02        35.01         1.02        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72        27.42        10.88         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09         0.95        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 
       18.84        75.25        50.37        58.39        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-6601 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
      100.01        11.74         2.14         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-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-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 
       22.03        22.98        16.01        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-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        12.03        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        17.75        18.25         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       15.58        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       38.20        92.75        49.91         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
       13.45         6.18        35.87        16.31        29.59        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        35.41        19.43       107.67        28.21        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GB 
       35.80        26.17        47.15        52.80        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        13.05        12.00        32.98         8.42        31.30 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 
       70.03        24.13        39.48        17.23        43.04        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       37.74        10.39        16.83        20.02        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 
       36.03         8.02         1.02        46.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        19.99        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       32.98         0.99         0.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 
       35.01        14.01        48.03        32.02         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
        0.99        20.98        13.94         6.02        37.02        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-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        38.04         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       26.43         1.81         6.05         6.97         9.37        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
        7.17        15.02        12.00        15.02        36.00        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
        5.29       126.44        57.24       129.27        24.13         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 
        8.45         9.96        37.51        31.30        32.19         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        55.76        47.08 

  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                          17.36                           19.66 
[1] "0.2 - 140.4 (17.4)" "0.0 - 139.2 (19.7)"
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   156  66
  DEL PEAK 46(22Q13.32) WILD-TYPE 286  96
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    156   66
  DEL PEAK 46(22Q13.32) WILD-TYPE  286   96
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON                            156                             286
  RECTUM                            66                              96
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 46(22Q13.32) MUTATED        29        0        9        58         1
  DEL PEAK 46(22Q13.32) WILD-TYPE      75        1       27       113         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(22Q13.32) MUTATED           1        10         12         31
  DEL PEAK 46(22Q13.32) WILD-TYPE         2        16          9         48
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(22Q13.32) MUTATED           24       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                               29                              75
  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                            31                              48
  STAGE IIIC                            24                              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  37 157  27
  DEL PEAK 46(22Q13.32) WILD-TYPE  16  70 256  39
D73V5, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  T1                             4                              16
  T2                            37                              70
  T3                           157                             256
  T4                            27                              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  71  51
  DEL PEAK 46(22Q13.32) WILD-TYPE 240  78  63
D73V6, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  N0                           102                             240
  N1                            71                              78
  N2                            51                              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"
D73V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   153  43
  DEL PEAK 46(22Q13.32) WILD-TYPE 295  43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    153   43
  DEL PEAK 46(22Q13.32) WILD-TYPE  295   43
   clus
vv  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  0                           153                             295
  1                            43                              43
[1] 2 2
[1] FALSE
D73V8, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   101 124
  DEL PEAK 46(22Q13.32) WILD-TYPE 185 198
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    101  124
  DEL PEAK 46(22Q13.32) WILD-TYPE  185  198
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  FEMALE                           101                             185
  MALE                             124                             198
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                    145
  DEL PEAK 46(22Q13.32) WILD-TYPE                  236
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                              11
  DEL PEAK 46(22Q13.32) WILD-TYPE                            49
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                      62
  DEL PEAK 46(22Q13.32) WILD-TYPE                    84
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                4
  DEL PEAK 46(22Q13.32) WILD-TYPE                              9
D73V9, multiclass
                                clus
vv                               DEL PEAK 46(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                     145
  COLON MUCINOUS ADENOCARCINOMA                             11
  RECTAL ADENOCARCINOMA                                     62
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       236
  COLON MUCINOUS ADENOCARCINOMA                               49
  RECTAL ADENOCARCINOMA                                       84
  RECTAL MUCINOUS ADENOCARCINOMA                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED     4 221
  DEL PEAK 46(22Q13.32) WILD-TYPE   5 378
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED      4  221
  DEL PEAK 46(22Q13.32) WILD-TYPE    5  378
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  NO                              4                               5
  YES                           221                             378
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(22Q13.32) MUTATED   153   2  17  12
  DEL PEAK 46(22Q13.32) WILD-TYPE 286   3  19  17
D73V11, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  R0                           153                             286
  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                          24   101
  DEL PEAK 46(22Q13.32) WILD-TYPE                        36   191
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 46(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 46(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     36
  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"
