[1] "ofn"        "-oTCOAD-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/COAD-TP/15076851/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/15082914/transformed.cor.cli.txt"

nPatients in clinical file=453, in cluster file=450, common to both=443
[1]  69 443
[1] "AMP PEAK  1(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           89                           354 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           89                           354 
[1] "AMP PEAK  2(5P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           357 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           357 
[1] "AMP PEAK  3(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           44                           399 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           44                           399 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           96                           347 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           96                           347 
[1] "AMP PEAK  5(7P21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          251                           192 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          251                           192 
[1] "AMP PEAK  6(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           156                            287 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           156                            287 
[1] "AMP PEAK  7(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           185                            258 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           185                            258 
[1] "AMP PEAK  8(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          231                           212 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          231                           212 
[1] "AMP PEAK  9(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           255                            188 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           255                            188 
[1] "AMP PEAK 10(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            91                            352 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            91                            352 
[1] "AMP PEAK 11(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            111                             332 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            111                             332 
[1] "AMP PEAK 12(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            270                             173 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            270                             173 
[1] "AMP PEAK 13(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           274                            169 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           274                            169 
[1] "AMP PEAK 14(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           123                            320 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           123                            320 
[1] "AMP PEAK 15(16Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           109                            334 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           109                            334 
[1] "AMP PEAK 16(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            44                            399 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            44                            399 
[1] "AMP PEAK 17(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         112                          331 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         112                          331 
[1] "AMP PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           104                            339 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           104                            339 
[1] "AMP PEAK 19(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            75                            368 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            75                            368 
[1] "AMP PEAK 20(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             94                             349 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             94                             349 
[1] "AMP PEAK 21(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           206                            237 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           206                            237 
[1] "AMP PEAK 22(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            248                             195 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            248                             195 
[1] "AMP PEAK 23(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            317                             126 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            317                             126 
[1] "AMP PEAK 24(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         318                          125 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         318                          125 
[1] "AMP PEAK 25(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            320                             123 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            320                             123 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           164                            279 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           164                            279 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        120                         323 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        120                         323 
[1] "DEL PEAK  3(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          115                           328 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          115                           328 
[1] "DEL PEAK  4(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         52                         391 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         52                         391 
[1] "DEL PEAK  5(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         427 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         427 
[1] "DEL PEAK  6(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           24                           419 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           24                           419 
[1] "DEL PEAK  7(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           69                           374 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           69                           374 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           85                           358 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           85                           358 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            399 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            399 
[1] "DEL PEAK 10(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          133                           310 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          133                           310 
[1] "DEL PEAK 11(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          145                           298 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          145                           298 
[1] "DEL PEAK 12(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          153                           290 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          153                           290 
[1] "DEL PEAK 13(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          103                           340 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          103                           340 
[1] "DEL PEAK 14(5Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          124                           319 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          124                           319 
[1] "DEL PEAK 15(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          127                           316 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          127                           316 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           389 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           389 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         61                         382 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         61                         382 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           431 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           431 
[1] "DEL PEAK 19(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          185                           258 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          185                           258 
[1] "DEL PEAK 20(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        199                         244 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        199                         244 
[1] "DEL PEAK 21(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           413 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           413 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           384 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           384 
[1] "DEL PEAK 23(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            77                            366 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            77                            366 
[1] "DEL PEAK 24(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            94                            349 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            94                            349 
[1] "DEL PEAK 25(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            106                             337 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            106                             337 
[1] "DEL PEAK 26(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           106                            337 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           106                            337 
[1] "DEL PEAK 27(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            59                            384 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            59                            384 
[1] "DEL PEAK 28(13Q14.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                             19                             424 
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                             19                             424 
[1] "DEL PEAK 29(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                           145                            298 
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                           145                            298 
[1] "DEL PEAK 30(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           173                            270 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           173                            270 
[1] "DEL PEAK 31(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           168                            275 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           168                            275 
[1] "DEL PEAK 32(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           165                            278 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           165                            278 
[1] "DEL PEAK 33(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            157                             286 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            157                             286 
[1] "DEL PEAK 34(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            54                            389 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            54                            389 
[1] "DEL PEAK 35(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            58                            385 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            58                            385 
[1] "DEL PEAK 36(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         248                          195 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         248                          195 
[1] "DEL PEAK 37(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            69                            374 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            69                            374 
[1] "DEL PEAK 38(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            241                             202 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            241                             202 
[1] "DEL PEAK 39(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           268                            175 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           268                            175 
[1] "DEL PEAK 40(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           282                            161 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           282                            161 
[1] "DEL PEAK 41(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            62                            381 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            62                            381 
[1] "DEL PEAK 42(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            83                            360 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            83                            360 
[1] "DEL PEAK 43(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           137                            306 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           137                            306 
[1] "DEL PEAK 44(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            156                             287 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            156                             287 
[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 443 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=81,	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=282,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=6,	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=13,	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=2,	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=21,	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   "1"                "264"                 
freq.contrast "264"              "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 21:'BATCH_NUMBER':	nDistinctValues=26,	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 443 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "COMPLETENESS_OF_RESECTION"             
[10] "NUMBER_OF_LYMPH_NODES"                 
[11] "RACE"                                  
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
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 
 11  78 301  52 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  78 301  52 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  78 301  52 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  78 301  52 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
257 104  81 
[1] "table(vv)"
vv
 N0  N1  N2 
257 104  81 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
257 104  81 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
257 104  81 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, 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=21, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(2Q33.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(2Q33.1) MUTATED    62  22
  AMP PEAK  1(2Q33.1) WILD-TYPE 275  71
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           84                           346 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           22                            71 
$`AMP PEAK  1(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 

$`AMP PEAK  1(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 
        8.42        31.30         9.70        70.03 

  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        74.56                        140.38 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        20.68                         20.35 
[1] "0.0 - 74.6 (20.7)"  "0.0 - 140.4 (20.4)"
[1] "hr=" "1.7"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(2Q33.1) MUTATED        13        0        5        19         0
  AMP PEAK  1(2Q33.1) WILD-TYPE      61        1       23       112         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(2Q33.1) MUTATED           1         5          3         14
  AMP PEAK  1(2Q33.1) WILD-TYPE         0        16          9         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(2Q33.1) MUTATED           12        9         4         1
  AMP PEAK  1(2Q33.1) WILD-TYPE         27       34        14         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  STAGE I                             13                            61
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           19                           112
  STAGE IIB                            0                             8
  STAGE IIC                            1                             0
  STAGE III                            5                            16
  STAGE IIIA                           3                             9
  STAGE IIIB                          14                            42
  STAGE IIIC                          12                            27
  STAGE IV                             9                            34
  STAGE IVA                            4                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(2Q33.1) MUTATED     3  14  63   9
  AMP PEAK  1(2Q33.1) WILD-TYPE   8  64 238  43
D1V4, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  T1                           3                             8
  T2                          14                            64
  T3                          63                           238
  T4                           9                            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(2Q33.1) MUTATED    40  22  26
  AMP PEAK  1(2Q33.1) WILD-TYPE 217  82  55
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  N0                          40                           217
  N1                          22                            82
  N2                          26                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    57  14
  AMP PEAK  1(2Q33.1) WILD-TYPE 265  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     57   14
  AMP PEAK  1(2Q33.1) WILD-TYPE  265   48
   clus
vv  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  0                          57                           265
  1                          14                            48
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    39  50
  AMP PEAK  1(2Q33.1) WILD-TYPE 171 183
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     39   50
  AMP PEAK  1(2Q33.1) WILD-TYPE  171  183
        clus
vv       AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  FEMALE                          39                           171
  MALE                            50                           183
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    79  10
  AMP PEAK  1(2Q33.1) WILD-TYPE 302  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     79   10
  AMP PEAK  1(2Q33.1) WILD-TYPE  302   50
                               clus
vv                              AMP PEAK  1(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                   79
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              AMP PEAK  1(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    302
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED     1  88
  AMP PEAK  1(2Q33.1) WILD-TYPE   2 352
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED      1   88
  AMP PEAK  1(2Q33.1) WILD-TYPE    2  352
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  NO                            1                             2
  YES                          88                           352
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(2Q33.1) MUTATED    56   2   6   6
  AMP PEAK  1(2Q33.1) WILD-TYPE 260   1  18  19
D1V10, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  R0                          56                           260
  R1                           2                             1
  R2                           6                            18
  RX                           6                            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"
D1V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(2Q33.1) MUTATED                                  1     2
  AMP PEAK  1(2Q33.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(2Q33.1) MUTATED                          14    47
  AMP PEAK  1(2Q33.1) WILD-TYPE                        40   164
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 14
  WHITE                                                     47
                                  clus
vv                                 AMP PEAK  1(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      164
[1] 4 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(5P13.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(5P13.2) MUTATED    66  18
  AMP PEAK  2(5P13.2) WILD-TYPE 271  75
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           84                           346 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           18                            75 
$`AMP PEAK  2(5P13.2) 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-A6-3807 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6650 TCGA-A6-6651 TCGA-AA-3488 
       34.65        32.45        30.44        20.61        21.76         5.03 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3666 
       26.01        12.99        13.02        24.00        19.99         2.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 
       47.01         5.98        37.05        19.00        19.04        37.02 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3966 
       14.93        36.03         0.99        17.03        24.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Z TCGA-AA-A01D 
       21.99        50.99        26.01        34.03        21.99        10.98 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 
       51.98         2.96         2.01        41.00        40.96         5.79 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-5403 TCGA-AZ-6598 
       16.44         0.92         0.20        18.84        62.79        49.41 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4752 
       29.56         1.94         2.24        49.08        25.02        13.02 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6169 
       16.01        15.02        14.04        29.03        14.99        13.02 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6924 
       11.01        19.59        17.75        17.13         7.53        14.30 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 
       13.41        12.00        11.38        12.59         7.50         6.12 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 
       98.24        95.18        13.38         1.55        35.41        82.39 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       91.79        46.75        47.15        12.79         8.42        30.28 

$`AMP PEAK  2(5P13.2) 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-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        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-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
        0.00        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       15.02        11.01        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3858 
       10.06         0.00        33.07         0.00        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-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
        2.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       38.04         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        5.03         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         0.72        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88         0.20         0.46        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        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-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         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-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-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-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       12.00        16.04        21.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        12.26        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25         1.32        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
        4.80        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.43         9.04         9.44        11.64         1.51        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-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       60.79       117.07         8.61        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-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
       13.25         0.53        19.43       107.67        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        52.80        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        13.05        12.00        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       32.98        31.30         9.70        70.03 

  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                        98.24                        140.38 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                       19.020                        20.995 
[1] "0.2 - 98.2 (19.0)"  "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  2(5P13.2) MUTATED        14        0        5        22         1
  AMP PEAK  2(5P13.2) WILD-TYPE      60        1       23       109         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(5P13.2) MUTATED           0         3          4          6
  AMP PEAK  2(5P13.2) WILD-TYPE         1        18          8         50
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(5P13.2) MUTATED           13       12         3         1
  AMP PEAK  2(5P13.2) WILD-TYPE         26       31        15         1
D2V3, multiclass
            clus
vv           AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  STAGE I                             14                            60
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           22                           109
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           4                             8
  STAGE IIIB                           6                            50
  STAGE IIIC                          13                            26
  STAGE IV                            12                            31
  STAGE IVA                            3                            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  2(5P13.2) MUTATED     1  18  60   7
  AMP PEAK  2(5P13.2) WILD-TYPE  10  60 241  45
D2V4, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  T1                           1                            10
  T2                          18                            60
  T3                          60                           241
  T4                           7                            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  2(5P13.2) MUTATED    42  20  24
  AMP PEAK  2(5P13.2) WILD-TYPE 215  84  57
D2V5, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  N0                          42                           215
  N1                          20                            84
  N2                          24                            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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    56  16
  AMP PEAK  2(5P13.2) WILD-TYPE 266  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     56   16
  AMP PEAK  2(5P13.2) WILD-TYPE  266   46
   clus
vv  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  0                          56                           266
  1                          16                            46
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    44  42
  AMP PEAK  2(5P13.2) WILD-TYPE 166 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     44   42
  AMP PEAK  2(5P13.2) WILD-TYPE  166  191
        clus
vv       AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  FEMALE                          44                           166
  MALE                            42                           191
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    74  12
  AMP PEAK  2(5P13.2) WILD-TYPE 307  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     74   12
  AMP PEAK  2(5P13.2) WILD-TYPE  307   48
                               clus
vv                              AMP PEAK  2(5P13.2) MUTATED
  COLON ADENOCARCINOMA                                   74
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              AMP PEAK  2(5P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    307
  COLON MUCINOUS ADENOCARCINOMA                            48
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED     0  86
  AMP PEAK  2(5P13.2) WILD-TYPE   3 354
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED      0   86
  AMP PEAK  2(5P13.2) WILD-TYPE    3  354
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  NO                            0                             3
  YES                          86                           354
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(5P13.2) MUTATED    63   0   8   2
  AMP PEAK  2(5P13.2) WILD-TYPE 253   3  16  23
D2V10, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  R0                          63                           253
  R1                           0                             3
  R2                           8                            16
  RX                           2                            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"
D2V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(5P13.2) MUTATED                                  1     1
  AMP PEAK  2(5P13.2) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(5P13.2) MUTATED                          11    41
  AMP PEAK  2(5P13.2) WILD-TYPE                        43   170
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(5P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     41
                                  clus
vv                                 AMP PEAK  2(5P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   43
  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(3) Variable = AMP PEAK  3(5Q22.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(5Q22.3) MUTATED    36   7
  AMP PEAK  3(5Q22.3) WILD-TYPE 301  86
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           43                           387 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                            7                            86 
$`AMP PEAK  3(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 
        9.70 

$`AMP PEAK  3(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 
       31.30        30.28        70.03 

  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         1.32                          0.00 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                       130.65                        140.38 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                        16.01                         21.01 
[1] "1.3 - 130.7 (16.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5Q22.3) MUTATED         7        0        2        11         1
  AMP PEAK  3(5Q22.3) WILD-TYPE      67        1       26       120         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(5Q22.3) MUTATED           0         1          1          4
  AMP PEAK  3(5Q22.3) WILD-TYPE         1        20         11         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(5Q22.3) MUTATED            5        6         5         0
  AMP PEAK  3(5Q22.3) WILD-TYPE         34       37        13         2
D3V3, multiclass
            clus
vv           AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  STAGE I                              7                            67
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           11                           120
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            11
  STAGE IIIB                           4                            52
  STAGE IIIC                           5                            34
  STAGE IV                             6                            37
  STAGE IVA                            5                            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  3(5Q22.3) MUTATED     1   8  29   6
  AMP PEAK  3(5Q22.3) WILD-TYPE  10  70 272  46
D3V4, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  T1                           1                            10
  T2                           8                            70
  T3                          29                           272
  T4                           6                            46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  3(5Q22.3) MUTATED    22  11  11
  AMP PEAK  3(5Q22.3) WILD-TYPE 235  93  70
D3V5, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  N0                          22                           235
  N1                          11                            93
  N2                          11                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    26  11
  AMP PEAK  3(5Q22.3) WILD-TYPE 296  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     26   11
  AMP PEAK  3(5Q22.3) WILD-TYPE  296   51
   clus
vv  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  0                          26                           296
  1                          11                            51
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    23  21
  AMP PEAK  3(5Q22.3) WILD-TYPE 187 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     23   21
  AMP PEAK  3(5Q22.3) WILD-TYPE  187  212
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  FEMALE                          23                           187
  MALE                            21                           212
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    41   3
  AMP PEAK  3(5Q22.3) WILD-TYPE 340  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     41    3
  AMP PEAK  3(5Q22.3) WILD-TYPE  340   57
                               clus
vv                              AMP PEAK  3(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                   41
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              AMP PEAK  3(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    340
  COLON MUCINOUS ADENOCARCINOMA                            57
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED     1  43
  AMP PEAK  3(5Q22.3) WILD-TYPE   2 397
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      1   43
  AMP PEAK  3(5Q22.3) WILD-TYPE    2  397
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  NO                            1                             2
  YES                          43                           397
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(5Q22.3) MUTATED    29   0   5   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 287   3  19  25
D3V10, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  R0                          29                           287
  R1                           0                             3
  R2                           5                            19
  RX                           0                            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"
D3V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(5Q22.3) MUTATED                                  0     0
  AMP PEAK  3(5Q22.3) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5Q22.3) MUTATED                           8    23
  AMP PEAK  3(5Q22.3) WILD-TYPE                        46   188
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     23
                                  clus
vv                                 AMP PEAK  3(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   46
  WHITE                                                      188
[1] 4 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(6P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(6P21.1) MUTATED    73  19
  AMP PEAK  4(6P21.1) WILD-TYPE 264  74
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           92                           338 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           19                            74 
$`AMP PEAK  4(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-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3846 
       19.99        15.02        85.05        10.06        35.05        17.03 
TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 
       10.06        24.03        27.02         2.01        20.98        21.99 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A01I 
       27.02         7.96        13.94        34.03        27.02        31.00 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 
        2.96        40.96        22.42         0.20        14.50         0.95 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 
        0.20        17.26        22.36        65.00         1.35        15.62 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       21.99         8.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 
       16.01         5.03        15.02        13.02        15.02        19.59 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       11.51         1.32        15.12        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA 
       10.13         9.04        13.41        11.38        13.32         7.50 
TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       14.04       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6310 
       13.45         1.55         0.53        28.21        82.39        45.11 
TCGA-G4-6311 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW 
       39.42        91.79        46.75        10.98        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL 
        9.70        30.28 

$`AMP PEAK  4(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-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        19.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 
        0.99        31.07        31.07        53.00        17.03        29.98 
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-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 
       24.00         2.01        34.03         2.01        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-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        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-A01K 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-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-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
        0.79         0.72         5.79        27.42        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09        16.31        15.75        21.44 
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-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
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-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-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-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        17.75        18.25        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.80        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        6.12        26.47        81.37       119.93        35.97        60.79 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67        13.25        35.41        19.43       107.67 
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-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80        18.18        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        13.05        12.00        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       31.30        70.03 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       117.07                        140.38 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       18.425                        20.995 
[1] "0.2 - 117.1 (18.4)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(6P21.1) MUTATED        13        0        1        24         1
  AMP PEAK  4(6P21.1) WILD-TYPE      61        1       27       107         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(6P21.1) MUTATED           0         4          6         15
  AMP PEAK  4(6P21.1) WILD-TYPE         1        17          6         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(6P21.1) MUTATED           13       10         6         1
  AMP PEAK  4(6P21.1) WILD-TYPE         26       33        12         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  STAGE I                             13                            61
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           24                           107
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             6
  STAGE IIIB                          15                            41
  STAGE IIIC                          13                            26
  STAGE IV                            10                            33
  STAGE IVA                            6                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(6P21.1) MUTATED     2  14  71   9
  AMP PEAK  4(6P21.1) WILD-TYPE   9  64 230  43
D4V4, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  T1                           2                             9
  T2                          14                            64
  T3                          71                           230
  T4                           9                            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  4(6P21.1) MUTATED    46  22  28
  AMP PEAK  4(6P21.1) WILD-TYPE 211  82  53
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          46                           211
  N1                          22                            82
  N2                          28                            53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    66  17
  AMP PEAK  4(6P21.1) WILD-TYPE 256  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     66   17
  AMP PEAK  4(6P21.1) WILD-TYPE  256   45
   clus
vv  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  0                          66                           256
  1                          17                            45
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    41  55
  AMP PEAK  4(6P21.1) WILD-TYPE 169 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     41   55
  AMP PEAK  4(6P21.1) WILD-TYPE  169  178
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          41                           169
  MALE                            55                           178
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    86   9
  AMP PEAK  4(6P21.1) WILD-TYPE 295  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     86    9
  AMP PEAK  4(6P21.1) WILD-TYPE  295   51
                               clus
vv                              AMP PEAK  4(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                   86
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              AMP PEAK  4(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    295
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED     3  93
  AMP PEAK  4(6P21.1) WILD-TYPE   0 347
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED      3   93
  AMP PEAK  4(6P21.1) WILD-TYPE    0  347
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                            3                             0
  YES                          93                           347
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(6P21.1) MUTATED    68   0   7   4
  AMP PEAK  4(6P21.1) WILD-TYPE 248   3  17  21
D4V10, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                          68                           248
  R1                           0                             3
  R2                           7                            17
  RX                           4                            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"
D4V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(6P21.1) MUTATED                                  1     1
  AMP PEAK  4(6P21.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(6P21.1) MUTATED                          11    53
  AMP PEAK  4(6P21.1) WILD-TYPE                        43   158
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     53
                                  clus
vv                                 AMP PEAK  4(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      158
[1] 4 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(7P21.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(7P21.2) MUTATED   189  54
  AMP PEAK  5(7P21.2) WILD-TYPE 148  39
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          243                           187 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                           54                            39 
$`AMP PEAK  5(7P21.2) 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-A6-2679 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-A01R TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H 
       35.01        33.04        26.01        37.02        51.98         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-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
       29.56         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        2.14         3.25         3.29         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       40.34        21.99        20.02        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        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-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       16.04        14.99        12.99        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 
       11.08        11.01        10.06        19.59        11.51        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       13.41        10.26        24.43        38.20        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 
       12.59       140.38         7.50        44.32       131.51         7.76 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
        6.12        14.04        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       13.38        13.45         1.55        33.67         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
      107.67        28.21        82.39        23.51        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        13.78        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5Z1 
       18.18         9.93        15.65        12.79        13.05         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
        9.70        30.28        70.03 

$`AMP PEAK  5(7P21.2) 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-A01S TCGA-AA-A01V 
       31.00        31.00        38.07         1.02         1.02        35.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
       39.06         2.96        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-CA-5254 TCGA-CA-6715 
       32.94         5.13         6.77       100.01         2.24         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        0.26         0.33         0.10        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-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 
       37.02        26.04        30.08        15.02        12.00        21.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       13.02        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6540 
       12.26        13.51        20.19        20.42        18.25        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       15.58        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A282 
       11.38       119.70       130.65        13.32       135.65       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 
       26.47        81.37       119.93        60.79        98.24        11.11 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.64         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       13.25        19.43         8.35        67.30        53.62        51.75 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U 
       22.09        26.04        35.80        26.17        52.80        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        19.33        12.00        42.77        29.46        32.98 
TCGA-QG-A5Z2 
       31.30 

  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                            0                             0 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                        20.61                         20.19 
[1] "0.0 - 140.4 (20.6)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.1"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(7P21.2) MUTATED        40        1       15        54         2
  AMP PEAK  5(7P21.2) WILD-TYPE      34        0       13        77         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(7P21.2) MUTATED           0        13         11         38
  AMP PEAK  5(7P21.2) WILD-TYPE         1         8          1         18
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(7P21.2) MUTATED           26       30        14         1
  AMP PEAK  5(7P21.2) WILD-TYPE         13       13         4         1
D5V3, multiclass
            clus
vv           AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  STAGE I                             40                            34
  STAGE IA                             1                             0
  STAGE II                            15                            13
  STAGE IIA                           54                            77
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                           13                             8
  STAGE IIIA                          11                             1
  STAGE IIIB                          38                            18
  STAGE IIIC                          26                            13
  STAGE IV                            30                            13
  STAGE IVA                           14                             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  5(7P21.2) MUTATED     9  42 170  29
  AMP PEAK  5(7P21.2) WILD-TYPE   2  36 131  23
D5V4, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  T1                           9                             2
  T2                          42                            36
  T3                         170                           131
  T4                          29                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  5(7P21.2) MUTATED   123  71  56
  AMP PEAK  5(7P21.2) WILD-TYPE 134  33  25
D5V5, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  N0                         123                           134
  N1                          71                            33
  N2                          56                            25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED   171  44
  AMP PEAK  5(7P21.2) WILD-TYPE 151  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED    171   44
  AMP PEAK  5(7P21.2) WILD-TYPE  151   18
   clus
vv  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  0                         171                           151
  1                          44                            18
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED   118 133
  AMP PEAK  5(7P21.2) WILD-TYPE  92 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED    118  133
  AMP PEAK  5(7P21.2) WILD-TYPE   92  100
        clus
vv       AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  FEMALE                         118                            92
  MALE                           133                           100
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED   224  26
  AMP PEAK  5(7P21.2) WILD-TYPE 157  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED    224   26
  AMP PEAK  5(7P21.2) WILD-TYPE  157   34
                               clus
vv                              AMP PEAK  5(7P21.2) MUTATED
  COLON ADENOCARCINOMA                                  224
  COLON MUCINOUS ADENOCARCINOMA                          26
                               clus
vv                              AMP PEAK  5(7P21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    157
  COLON MUCINOUS ADENOCARCINOMA                            34
[1] 2 2
[1] FALSE
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED     3 248
  AMP PEAK  5(7P21.2) WILD-TYPE   0 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED      3  248
  AMP PEAK  5(7P21.2) WILD-TYPE    0  192
     clus
vv    AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  NO                            3                             0
  YES                         248                           192
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(7P21.2) MUTATED   179   2  16  10
  AMP PEAK  5(7P21.2) WILD-TYPE 137   1   8  15
D5V10, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  R0                         179                           137
  R1                           2                             1
  R2                          16                             8
  RX                          10                            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"
D5V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(7P21.2) MUTATED                                  1     5
  AMP PEAK  5(7P21.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(7P21.2) MUTATED                          35   124
  AMP PEAK  5(7P21.2) WILD-TYPE                        19    87
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(7P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    124
                                  clus
vv                                 AMP PEAK  5(7P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                       87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(8P11.23) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8P11.23) MUTATED   119  29
  AMP PEAK  6(8P11.23) WILD-TYPE 218  64
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           148                            282 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                            29                             64 
$`AMP PEAK  6(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 
       32.98         8.42        30.28        70.03 

$`AMP PEAK  6(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 

  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                             0                              0 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                        119.70                         140.38 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                        19.020                         21.875 
[1] "0.0 - 119.7 (19.0)" "0.0 - 140.4 (21.9)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(8P11.23) MUTATED        31        0       15        39         3
  AMP PEAK  6(8P11.23) WILD-TYPE      43        1       13        92         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8P11.23) MUTATED           1         8          4         18
  AMP PEAK  6(8P11.23) WILD-TYPE         0        13          8         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8P11.23) MUTATED           16       14         6         0
  AMP PEAK  6(8P11.23) WILD-TYPE         23       29        12         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  STAGE I                              31                             43
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            39                             92
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            4                              8
  STAGE IIIB                           18                             38
  STAGE IIIC                           16                             23
  STAGE IV                             14                             29
  STAGE IVA                             6                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(8P11.23) MUTATED     3  31 105  17
  AMP PEAK  6(8P11.23) WILD-TYPE   8  47 196  35
D6V4, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  T1                            3                              8
  T2                           31                             47
  T3                          105                            196
  T4                           17                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  6(8P11.23) MUTATED    94  33  29
  AMP PEAK  6(8P11.23) WILD-TYPE 163  71  52
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  N0                           94                            163
  N1                           33                             71
  N2                           29                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   111  20
  AMP PEAK  6(8P11.23) WILD-TYPE 211  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    111   20
  AMP PEAK  6(8P11.23) WILD-TYPE  211   42
   clus
vv  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  0                          111                            211
  1                           20                             42
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED    76  80
  AMP PEAK  6(8P11.23) WILD-TYPE 134 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED     76   80
  AMP PEAK  6(8P11.23) WILD-TYPE  134  153
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  FEMALE                           76                            134
  MALE                             80                            153
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   139  17
  AMP PEAK  6(8P11.23) WILD-TYPE 242  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    139   17
  AMP PEAK  6(8P11.23) WILD-TYPE  242   43
                               clus
vv                              AMP PEAK  6(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                   139
  COLON MUCINOUS ADENOCARCINOMA                           17
                               clus
vv                              AMP PEAK  6(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                     242
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED     2 154
  AMP PEAK  6(8P11.23) WILD-TYPE   1 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED      2  154
  AMP PEAK  6(8P11.23) WILD-TYPE    1  286
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  NO                             2                              1
  YES                          154                            286
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8P11.23) MUTATED   113   1   9  12
  AMP PEAK  6(8P11.23) WILD-TYPE 203   2  15  13
D6V10, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  R0                          113                            203
  R1                            1                              2
  R2                            9                             15
  RX                           12                             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"
D6V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(8P11.23) MUTATED                                  0     5
  AMP PEAK  6(8P11.23) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8P11.23) MUTATED                          17    81
  AMP PEAK  6(8P11.23) WILD-TYPE                        37   130
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      81
                                  clus
vv                                 AMP PEAK  6(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(8P11.21) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.21) MUTATED   142  35
  AMP PEAK  7(8P11.21) WILD-TYPE 195  58
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           177                            253 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                            35                             58 
$`AMP PEAK  7(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-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        29.16        27.09        25.08        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-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
       21.99        12.00         1.02        37.02        51.98         0.92 
TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00         0.07         4.21         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 
       16.44         0.92        27.09        21.44        17.26        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-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
        2.14         3.29         0.07         1.35       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       49.08        51.32         2.01        20.02        37.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 
        5.03        15.02        15.02        15.02        29.03        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       12.99        13.02        11.01        11.08        11.08        10.06 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       11.51        20.19         1.32        43.27         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04        13.41        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28K TCGA-F4-6459 
      130.65         7.50        44.32         6.12        98.24         8.61 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 
       13.64        13.45         6.18        16.31        16.24         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 
       67.30        53.62        44.68        45.11        39.42        26.43 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YW TCGA-QG-A5YX 
       46.75        47.15        18.18        10.98        29.46        32.98 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
        8.42        30.28        70.03 

$`AMP PEAK  7(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-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13         8.38        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-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       39.06         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.72        10.88         0.20         0.46        14.50        16.31 
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-4614 
       18.84        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5796 
       65.00         6.77        12.10       100.01        29.56         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.14         2.93       124.27        23.05        26.04 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       13.02        29.06        22.03        17.03        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       16.04        21.99        15.02        14.04        12.95        13.05 
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-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.42        17.75        18.25        15.12        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
       12.39         9.44        11.64         1.51        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 
      119.93        35.97        60.79       117.07        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       11.11        35.87         1.55        29.59        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        65.85        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        91.79        52.80        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 
       15.65        12.79        13.05        12.00        42.77        31.30 
TCGA-QL-A97D 
        9.70 

  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                         19.00                          21.99 
[1] "0.0 - 130.7 (19.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(8P11.21) MUTATED        33        0       17        50         3
  AMP PEAK  7(8P11.21) WILD-TYPE      41        1       11        81         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.21) MUTATED           1         9          5         23
  AMP PEAK  7(8P11.21) WILD-TYPE         0        12          7         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.21) MUTATED           13       22         7         0
  AMP PEAK  7(8P11.21) WILD-TYPE         26       21        11         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  STAGE I                              33                             41
  STAGE IA                              0                              1
  STAGE II                             17                             11
  STAGE IIA                            50                             81
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             9                             12
  STAGE IIIA                            5                              7
  STAGE IIIB                           23                             33
  STAGE IIIC                           13                             26
  STAGE IV                             22                             21
  STAGE IVA                             7                             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  7(8P11.21) MUTATED     3  35 128  19
  AMP PEAK  7(8P11.21) WILD-TYPE   8  43 173  33
D7V4, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  T1                            3                              8
  T2                           35                             43
  T3                          128                            173
  T4                           19                             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
  AMP PEAK  7(8P11.21) MUTATED   112  39  33
  AMP PEAK  7(8P11.21) WILD-TYPE 145  65  48
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  N0                          112                            145
  N1                           39                             65
  N2                           33                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   131  29
  AMP PEAK  7(8P11.21) WILD-TYPE 191  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    131   29
  AMP PEAK  7(8P11.21) WILD-TYPE  191   33
   clus
vv  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  0                          131                            191
  1                           29                             33
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED    81 104
  AMP PEAK  7(8P11.21) WILD-TYPE 129 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED     81  104
  AMP PEAK  7(8P11.21) WILD-TYPE  129  129
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  FEMALE                           81                            129
  MALE                            104                            129
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   163  22
  AMP PEAK  7(8P11.21) WILD-TYPE 218  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    163   22
  AMP PEAK  7(8P11.21) WILD-TYPE  218   38
                               clus
vv                              AMP PEAK  7(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                   163
  COLON MUCINOUS ADENOCARCINOMA                           22
                               clus
vv                              AMP PEAK  7(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     218
  COLON MUCINOUS ADENOCARCINOMA                             38
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED     2 183
  AMP PEAK  7(8P11.21) WILD-TYPE   1 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED      2  183
  AMP PEAK  7(8P11.21) WILD-TYPE    1  257
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  NO                             2                              1
  YES                          183                            257
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.21) MUTATED   133   0  13  13
  AMP PEAK  7(8P11.21) WILD-TYPE 183   3  11  12
D7V10, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  R0                          133                            183
  R1                            0                              3
  R2                           13                             11
  RX                           13                             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"
D7V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(8P11.21) MUTATED                                  0     6
  AMP PEAK  7(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8P11.21) MUTATED                          19    96
  AMP PEAK  7(8P11.21) WILD-TYPE                        35   115
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK  7(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(8Q12.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(8Q12.1) MUTATED   177  45
  AMP PEAK  8(8Q12.1) WILD-TYPE 160  48
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          222                           208 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                           45                            48 
$`AMP PEAK  8(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-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 
       45.60        13.94        37.25        37.02        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        31.63        29.19        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        24.16        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       20.28         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3529 
       35.01         6.97         1.02        36.03        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       13.02        24.00        20.98        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
        5.98        37.05        36.00         5.03        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 
       10.06        36.95        37.02        17.03        33.07         0.00 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 
       18.05         2.01        12.99        24.00        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-A00L TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z 
       19.00        18.05        38.04         0.99        17.03        21.99 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J 
       12.00        31.00         1.02        51.98         2.96         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
        0.92        41.00         0.07         5.79        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-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       17.26        18.84        75.25        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        61.41        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
        3.06         2.14         0.07         1.35       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       49.08        51.32         2.01        20.02        37.02        25.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 
       13.02        11.01        11.08        11.08        10.06        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        11.51        20.19         1.32        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        4.80        17.13        16.14        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        38.20       130.65       140.38         7.50        44.32 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
        6.12        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
       13.38        13.64        13.45         6.18        16.31        16.24 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        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-A6GA 
       26.43        46.75        47.15        18.18        10.98         9.93 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
       15.65        29.46        32.98         8.42        30.28        70.03 

$`AMP PEAK  8(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-A6-2683 TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 
       16.57        37.05        34.65        14.53        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 
       23.61        22.09        22.06        22.52         8.38        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 
       61.84        56.25         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-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 
       29.95        23.01        19.99        13.94        61.02         2.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 
        0.92        47.05        11.01        19.00        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-3844 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       38.99        14.93         0.00        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       32.05        31.07        53.00        31.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       24.00         2.01        20.98        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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       34.03        18.05         4.01        27.02        42.02        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        39.98         2.01        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 
        0.72        22.42        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-4614 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 
        1.41         5.65         6.77       100.01         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.14         2.93       124.27        23.05        26.04 
TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       22.03        12.00        16.04        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 
       13.05        11.01        12.03        45.40        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 
       17.75        18.25        17.85        12.49        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.64         1.51        12.00        24.43        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 
       14.04        26.47        81.37       119.93        95.18        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        29.59        33.67        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-A6GC TCGA-NH-A8F7 
       91.79        52.80        19.33        19.33        12.79        13.05 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D 
       12.00        42.77        31.30         9.70 

  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                       19.040                        21.565 
[1] "0.0 - 140.4 (19.0)" "0.0 - 139.2 (21.6)"
[1] "hr=" "1.1"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8Q12.1) MUTATED        37        0       16        64         3
  AMP PEAK  8(8Q12.1) WILD-TYPE      37        1       12        67         5
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8Q12.1) MUTATED           1         9          8         31
  AMP PEAK  8(8Q12.1) WILD-TYPE         0        12          4         25
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8Q12.1) MUTATED           21       27        11         0
  AMP PEAK  8(8Q12.1) WILD-TYPE         18       16         7         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  STAGE I                             37                            37
  STAGE IA                             0                             1
  STAGE II                            16                            12
  STAGE IIA                           64                            67
  STAGE IIB                            3                             5
  STAGE IIC                            1                             0
  STAGE III                            9                            12
  STAGE IIIA                           8                             4
  STAGE IIIB                          31                            25
  STAGE IIIC                          21                            18
  STAGE IV                            27                            16
  STAGE IVA                           11                             7
  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(8Q12.1) MUTATED     4  41 161  25
  AMP PEAK  8(8Q12.1) WILD-TYPE   7  37 140  27
D8V4, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  T1                           4                             7
  T2                          41                            37
  T3                         161                           140
  T4                          25                            27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  8(8Q12.1) MUTATED   130  54  47
  AMP PEAK  8(8Q12.1) WILD-TYPE 127  50  34
D8V5, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  N0                         130                           127
  N1                          54                            50
  N2                          47                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   161  38
  AMP PEAK  8(8Q12.1) WILD-TYPE 161  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    161   38
  AMP PEAK  8(8Q12.1) WILD-TYPE  161   24
   clus
vv  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  0                         161                           161
  1                          38                            24
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   106 125
  AMP PEAK  8(8Q12.1) WILD-TYPE 104 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    106  125
  AMP PEAK  8(8Q12.1) WILD-TYPE  104  108
        clus
vv       AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  FEMALE                         106                           104
  MALE                           125                           108
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   207  24
  AMP PEAK  8(8Q12.1) WILD-TYPE 174  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    207   24
  AMP PEAK  8(8Q12.1) WILD-TYPE  174   36
                               clus
vv                              AMP PEAK  8(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                  207
  COLON MUCINOUS ADENOCARCINOMA                          24
                               clus
vv                              AMP PEAK  8(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    174
  COLON MUCINOUS ADENOCARCINOMA                            36
[1] 2 2
[1] FALSE
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED     3 228
  AMP PEAK  8(8Q12.1) WILD-TYPE   0 212
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED      3  228
  AMP PEAK  8(8Q12.1) WILD-TYPE    0  212
     clus
vv    AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  NO                            3                             0
  YES                         228                           212
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(8Q12.1) MUTATED   161   1  16  14
  AMP PEAK  8(8Q12.1) WILD-TYPE 155   2   8  11
D8V10, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  R0                         161                           155
  R1                           1                             2
  R2                          16                             8
  RX                          14                            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"
D8V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(8Q12.1) MUTATED                                  0     5
  AMP PEAK  8(8Q12.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q12.1) MUTATED                          28   119
  AMP PEAK  8(8Q12.1) WILD-TYPE                        26    92
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    119
                                  clus
vv                                 AMP PEAK  8(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                       92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(8Q24.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.21) MUTATED   193  53
  AMP PEAK  9(8Q24.21) WILD-TYPE 144  40
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           246                            184 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            53                             40 
$`AMP PEAK  9(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 

$`AMP PEAK  9(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 
       13.05        42.77        31.30         9.70 

  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        20.005                         21.450 
[1] "0.0 - 140.4 (20.0)" "0.0 - 139.2 (21.5)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(8Q24.21) MUTATED        41        0       18        68         3
  AMP PEAK  9(8Q24.21) WILD-TYPE      33        1       10        63         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(8Q24.21) MUTATED           1        10         10         34
  AMP PEAK  9(8Q24.21) WILD-TYPE         0        11          2         22
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q24.21) MUTATED           22       31        13         0
  AMP PEAK  9(8Q24.21) WILD-TYPE         17       12         5         2
D9V3, multiclass
            clus
vv           AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  STAGE I                              41                             33
  STAGE IA                              0                              1
  STAGE II                             18                             10
  STAGE IIA                            68                             63
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                            10                             11
  STAGE IIIA                           10                              2
  STAGE IIIB                           34                             22
  STAGE IIIC                           22                             17
  STAGE IV                             31                             12
  STAGE IVA                            13                              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  9(8Q24.21) MUTATED     4  47 177  27
  AMP PEAK  9(8Q24.21) WILD-TYPE   7  31 124  25
D9V4, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  T1                            4                              7
  T2                           47                             31
  T3                          177                            124
  T4                           27                             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
  AMP PEAK  9(8Q24.21) MUTATED   144  57  53
  AMP PEAK  9(8Q24.21) WILD-TYPE 113  47  28
D9V5, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  N0                          144                            113
  N1                           57                             47
  N2                           53                             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"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   178  44
  AMP PEAK  9(8Q24.21) WILD-TYPE 144  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    178   44
  AMP PEAK  9(8Q24.21) WILD-TYPE  144   18
   clus
vv  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  0                          178                            144
  1                           44                             18
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   115 140
  AMP PEAK  9(8Q24.21) WILD-TYPE  95  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    115  140
  AMP PEAK  9(8Q24.21) WILD-TYPE   95   93
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  FEMALE                          115                             95
  MALE                            140                             93
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   225  29
  AMP PEAK  9(8Q24.21) WILD-TYPE 156  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    225   29
  AMP PEAK  9(8Q24.21) WILD-TYPE  156   31
                               clus
vv                              AMP PEAK  9(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                   225
  COLON MUCINOUS ADENOCARCINOMA                           29
                               clus
vv                              AMP PEAK  9(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     156
  COLON MUCINOUS ADENOCARCINOMA                             31
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED     3 252
  AMP PEAK  9(8Q24.21) WILD-TYPE   0 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED      3  252
  AMP PEAK  9(8Q24.21) WILD-TYPE    0  188
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  NO                             3                              0
  YES                          252                            188
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8Q24.21) MUTATED   177   1  17  16
  AMP PEAK  9(8Q24.21) WILD-TYPE 139   2   7   9
D9V10, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  R0                          177                            139
  R1                            1                              2
  R2                           17                              7
  RX                           16                              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"
D9V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.21) MUTATED                                  0     7
  AMP PEAK  9(8Q24.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.21) MUTATED                          30   130
  AMP PEAK  9(8Q24.21) WILD-TYPE                        24    81
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  30
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK  9(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                        81
[1] 4 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(11P15.5) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(11P15.5) MUTATED    70  19
  AMP PEAK 10(11P15.5) WILD-TYPE 267  74
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            89                            341 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            19                             74 
$`AMP PEAK 10(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 
       45.11        35.93        42.77        29.46        30.28 

$`AMP PEAK 10(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 
       32.98         8.42        31.30         9.70        70.03 

  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                             0                              0 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                         21.99                          20.19 
[1] "0.0 - 102.4 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(11P15.5) MUTATED        11        0        4        21         1
  AMP PEAK 10(11P15.5) WILD-TYPE      63        1       24       110         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(11P15.5) MUTATED           0         4          4         14
  AMP PEAK 10(11P15.5) WILD-TYPE         1        17          8         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(11P15.5) MUTATED           12       12         6         0
  AMP PEAK 10(11P15.5) WILD-TYPE         27       31        12         2
D10V3, multiclass
            clus
vv           AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  STAGE I                              11                             63
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            21                            110
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            4                              8
  STAGE IIIB                           14                             42
  STAGE IIIC                           12                             27
  STAGE IV                             12                             31
  STAGE IVA                             6                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 10(11P15.5) MUTATED     3  16  67   5
  AMP PEAK 10(11P15.5) WILD-TYPE   8  62 234  47
D10V4, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  T1                            3                              8
  T2                           16                             62
  T3                           67                            234
  T4                            5                             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 10(11P15.5) MUTATED    42  26  22
  AMP PEAK 10(11P15.5) WILD-TYPE 215  78  59
D10V5, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  N0                           42                            215
  N1                           26                             78
  N2                           22                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    63  18
  AMP PEAK 10(11P15.5) WILD-TYPE 259  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     63   18
  AMP PEAK 10(11P15.5) WILD-TYPE  259   44
   clus
vv  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  0                           63                            259
  1                           18                             44
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    45  46
  AMP PEAK 10(11P15.5) WILD-TYPE 165 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     45   46
  AMP PEAK 10(11P15.5) WILD-TYPE  165  187
        clus
vv       AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  FEMALE                           45                            165
  MALE                             46                            187
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    85   4
  AMP PEAK 10(11P15.5) WILD-TYPE 296  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     85    4
  AMP PEAK 10(11P15.5) WILD-TYPE  296   56
                               clus
vv                              AMP PEAK 10(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                    85
  COLON MUCINOUS ADENOCARCINOMA                            4
                               clus
vv                              AMP PEAK 10(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                     296
  COLON MUCINOUS ADENOCARCINOMA                             56
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED     2  89
  AMP PEAK 10(11P15.5) WILD-TYPE   1 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED      2   89
  AMP PEAK 10(11P15.5) WILD-TYPE    1  351
     clus
vv    AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  NO                             2                              1
  YES                           89                            351
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11P15.5) MUTATED    62   1   7   6
  AMP PEAK 10(11P15.5) WILD-TYPE 254   2  17  19
D10V10, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  R0                           62                            254
  R1                            1                              2
  R2                            7                             17
  RX                            6                             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"
D10V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(11P15.5) MUTATED                                  0     4
  AMP PEAK 10(11P15.5) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(11P15.5) MUTATED                           7    41
  AMP PEAK 10(11P15.5) WILD-TYPE                        47   170
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      41
                                  clus
vv                                 AMP PEAK 10(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    47
  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(11) Variable = AMP PEAK 11(12P13.33) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 11(12P13.33) MUTATED    79  26
  AMP PEAK 11(12P13.33) WILD-TYPE 258  67
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            105                             325 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             26                              67 
$`AMP PEAK 11(12P13.33) 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-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 
       15.62        51.32         2.01        20.02        25.02        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 
       16.01        15.02        15.02        21.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6539 
       11.01        11.01        20.19        17.75         4.80        12.49 
TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 
       15.58        14.30        11.64        13.41        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 
      119.70        24.43        13.32        44.32        95.18         8.61 
TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6627 
       35.87        16.31        44.68        35.93        13.78        47.15 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D 
       10.98        15.65         9.70 

$`AMP PEAK 11(12P13.33) 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-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.99        21.14         2.93       124.27        23.05        37.02 
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-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.98        15.02         5.03        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        29.03        16.04        14.99        12.99        15.02 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25         1.32        43.27        15.12        17.85        17.13 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       16.14         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        9.44         1.51        11.38        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59       140.38         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-F4-6460 
      119.93        35.97        60.79       117.07        98.24        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 
       11.11        13.64        13.45         6.18         1.55        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-G4-6299 
      107.67        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       67.30        65.85        53.62        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        46.75        52.80        18.18 
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-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        30.28 
TCGA-WS-AB45 
       70.03 

  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                              0                               0 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                          16.31                           21.99 
[1] "0.0 - 119.7 (16.3)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(12P13.33) MUTATED        14        1        9        40         2
  AMP PEAK 11(12P13.33) WILD-TYPE      60        0       19        91         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(12P13.33) MUTATED           0         5          5          6
  AMP PEAK 11(12P13.33) WILD-TYPE         1        16          7         50
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(12P13.33) MUTATED           10       11         6         0
  AMP PEAK 11(12P13.33) WILD-TYPE         29       32        12         2
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  STAGE I                               14                              60
  STAGE IA                               1                               0
  STAGE II                               9                              19
  STAGE IIA                             40                              91
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             5                               7
  STAGE IIIB                             6                              50
  STAGE IIIC                            10                              29
  STAGE IV                              11                              32
  STAGE IVA                              6                              12
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 11(12P13.33) MUTATED     0  17  77  16
  AMP PEAK 11(12P13.33) WILD-TYPE  11  61 224  36
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  T1                             0                              11
  T2                            17                              61
  T3                            77                             224
  T4                            16                              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 11(12P13.33) MUTATED    70  20  21
  AMP PEAK 11(12P13.33) WILD-TYPE 187  84  60
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  N0                            70                             187
  N1                            20                              84
  N2                            21                              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"
D11V6, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    78  17
  AMP PEAK 11(12P13.33) WILD-TYPE 244  45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     78   17
  AMP PEAK 11(12P13.33) WILD-TYPE  244   45
   clus
vv  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  0                            78                             244
  1                            17                              45
[1] 2 2
[1] FALSE
D11V7, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    54  57
  AMP PEAK 11(12P13.33) WILD-TYPE 156 176
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     54   57
  AMP PEAK 11(12P13.33) WILD-TYPE  156  176
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  FEMALE                            54                             156
  MALE                              57                             176
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    97  14
  AMP PEAK 11(12P13.33) WILD-TYPE 284  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     97   14
  AMP PEAK 11(12P13.33) WILD-TYPE  284   46
                               clus
vv                              AMP PEAK 11(12P13.33) MUTATED
  COLON ADENOCARCINOMA                                     97
  COLON MUCINOUS ADENOCARCINOMA                            14
                               clus
vv                              AMP PEAK 11(12P13.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      284
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED     0 111
  AMP PEAK 11(12P13.33) WILD-TYPE   3 329
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED      0  111
  AMP PEAK 11(12P13.33) WILD-TYPE    3  329
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  NO                              0                               3
  YES                           111                             329
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 11(12P13.33) MUTATED    81   1   3   5
  AMP PEAK 11(12P13.33) WILD-TYPE 235   2  21  20
D11V10, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  R0                            81                             235
  R1                             1                               2
  R2                             3                              21
  RX                             5                              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"
D11V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(12P13.33) MUTATED                                  0     1
  AMP PEAK 11(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P13.33) MUTATED                          12    55
  AMP PEAK 11(12P13.33) WILD-TYPE                        42   156
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       55
                                  clus
vv                                 AMP PEAK 11(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     42
  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(12) Variable = AMP PEAK 12(13Q12.13) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 12(13Q12.13) MUTATED   207  55
  AMP PEAK 12(13Q12.13) WILD-TYPE 130  38
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            262                             168 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                             55                              38 
$`AMP PEAK 12(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 
       32.98         8.42         9.70        30.28 

$`AMP PEAK 12(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 

  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                         20.445                          20.305 
[1] "0.1 - 131.5 (20.4)" "0.0 - 140.4 (20.3)"
[1] "hr=" "1"  
D12V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(13Q12.13) MUTATED        43        0       14        68         2
  AMP PEAK 12(13Q12.13) WILD-TYPE      31        1       14        63         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(13Q12.13) MUTATED           1        11         11         39
  AMP PEAK 12(13Q12.13) WILD-TYPE         0        10          1         17
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(13Q12.13) MUTATED           25       36        15         0
  AMP PEAK 12(13Q12.13) WILD-TYPE         14        7         3         2
D12V3, multiclass
            clus
vv           AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  STAGE I                               43                              31
  STAGE IA                               0                               1
  STAGE II                              14                              14
  STAGE IIA                             68                              63
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                             11                              10
  STAGE IIIA                            11                               1
  STAGE IIIB                            39                              17
  STAGE IIIC                            25                              14
  STAGE IV                              36                               7
  STAGE IVA                             15                               3
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 12(13Q12.13) MUTATED     7  46 187  30
  AMP PEAK 12(13Q12.13) WILD-TYPE   4  32 114  22
D12V4, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  T1                             7                               4
  T2                            46                              32
  T3                           187                             114
  T4                            30                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 12(13Q12.13) MUTATED   138  76  56
  AMP PEAK 12(13Q12.13) WILD-TYPE 119  28  25
D12V5, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  N0                           138                             119
  N1                            76                              28
  N2                            56                              25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   186  50
  AMP PEAK 12(13Q12.13) WILD-TYPE 136  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    186   50
  AMP PEAK 12(13Q12.13) WILD-TYPE  136   12
   clus
vv  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  0                           186                             136
  1                            50                              12
[1] 2 2
[1] FALSE
D12V7, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   126 144
  AMP PEAK 12(13Q12.13) WILD-TYPE  84  89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    126  144
  AMP PEAK 12(13Q12.13) WILD-TYPE   84   89
        clus
vv       AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  FEMALE                           126                              84
  MALE                             144                              89
[1] 2 2
[1] FALSE
D12V8, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   251  18
  AMP PEAK 12(13Q12.13) WILD-TYPE 130  42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    251   18
  AMP PEAK 12(13Q12.13) WILD-TYPE  130   42
                               clus
vv                              AMP PEAK 12(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                    251
  COLON MUCINOUS ADENOCARCINOMA                            18
                               clus
vv                              AMP PEAK 12(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      130
  COLON MUCINOUS ADENOCARCINOMA                              42
[1] 2 2
[1] FALSE
D12V9, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED     3 267
  AMP PEAK 12(13Q12.13) WILD-TYPE   0 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED      3  267
  AMP PEAK 12(13Q12.13) WILD-TYPE    0  173
     clus
vv    AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  NO                              3                               0
  YES                           267                             173
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 12(13Q12.13) MUTATED   191   1  19  10
  AMP PEAK 12(13Q12.13) WILD-TYPE 125   2   5  15
D12V10, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  R0                           191                             125
  R1                             1                               2
  R2                            19                               5
  RX                            10                              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"
D12V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(13Q12.13) MUTATED                                  0     4
  AMP PEAK 12(13Q12.13) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(13Q12.13) MUTATED                          33   135
  AMP PEAK 12(13Q12.13) WILD-TYPE                        21    76
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      135
                                  clus
vv                                 AMP PEAK 12(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                         76
[1] 4 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(13Q22.1) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(13Q22.1) MUTATED   209  57
  AMP PEAK 13(13Q22.1) WILD-TYPE 128  36
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           266                            164 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                            57                             36 
$`AMP PEAK 13(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 
        9.70        30.28 

$`AMP PEAK 13(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 
       31.30        70.03 

  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                         19.79                          22.01 
[1] "0.1 - 131.5 (19.8)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q22.1) MUTATED        45        0       15        66         2
  AMP PEAK 13(13Q22.1) WILD-TYPE      29        1       13        65         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(13Q22.1) MUTATED           1        12         11         39
  AMP PEAK 13(13Q22.1) WILD-TYPE         0         9          1         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(13Q22.1) MUTATED           27       35        15         0
  AMP PEAK 13(13Q22.1) WILD-TYPE         12        8         3         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  STAGE I                              45                             29
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            66                             65
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            12                              9
  STAGE IIIA                           11                              1
  STAGE IIIB                           39                             17
  STAGE IIIC                           27                             12
  STAGE IV                             35                              8
  STAGE IVA                            15                              3
  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(13Q22.1) MUTATED     8  48 187  31
  AMP PEAK 13(13Q22.1) WILD-TYPE   3  30 114  21
D13V4, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  T1                            8                              3
  T2                           48                             30
  T3                          187                            114
  T4                           31                             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 13(13Q22.1) MUTATED   139  77  57
  AMP PEAK 13(13Q22.1) WILD-TYPE 118  27  24
D13V5, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  N0                          139                            118
  N1                           77                             27
  N2                           57                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED   188  49
  AMP PEAK 13(13Q22.1) WILD-TYPE 134  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED    188   49
  AMP PEAK 13(13Q22.1) WILD-TYPE  134   13
   clus
vv  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  0                          188                            134
  1                           49                             13
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED   124 150
  AMP PEAK 13(13Q22.1) WILD-TYPE  86  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED    124  150
  AMP PEAK 13(13Q22.1) WILD-TYPE   86   83
        clus
vv       AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  FEMALE                          124                             86
  MALE                            150                             83
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED   253  20
  AMP PEAK 13(13Q22.1) WILD-TYPE 128  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED    253   20
  AMP PEAK 13(13Q22.1) WILD-TYPE  128   40
                               clus
vv                              AMP PEAK 13(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   253
  COLON MUCINOUS ADENOCARCINOMA                           20
                               clus
vv                              AMP PEAK 13(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     128
  COLON MUCINOUS ADENOCARCINOMA                             40
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED     3 271
  AMP PEAK 13(13Q22.1) WILD-TYPE   0 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED      3  271
  AMP PEAK 13(13Q22.1) WILD-TYPE    0  169
     clus
vv    AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  NO                             3                              0
  YES                          271                            169
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(13Q22.1) MUTATED   193   1  18  10
  AMP PEAK 13(13Q22.1) WILD-TYPE 123   2   6  15
D13V10, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  R0                          193                            123
  R1                            1                              2
  R2                           18                              6
  RX                           10                             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"
D13V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(13Q22.1) MUTATED                                  0     4
  AMP PEAK 13(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(13Q22.1) MUTATED                          34   138
  AMP PEAK 13(13Q22.1) WILD-TYPE                        20    73
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  34
  WHITE                                                     138
                                  clus
vv                                 AMP PEAK 13(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                        73
[1] 4 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(16P11.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(16P11.2) MUTATED    96  22
  AMP PEAK 14(16P11.2) WILD-TYPE 241  71
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           118                            312 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                            22                             71 
$`AMP PEAK 14(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 
       46.75        15.65        12.79         9.70 

$`AMP PEAK 14(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 

  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                             0                              0 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                        21.485                         20.155 
[1] "0.0 - 102.4 (21.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(16P11.2) MUTATED        14        1        3        29         1
  AMP PEAK 14(16P11.2) WILD-TYPE      60        0       25       102         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(16P11.2) MUTATED           0         5          9         20
  AMP PEAK 14(16P11.2) WILD-TYPE         1        16          3         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(16P11.2) MUTATED           16       15         5         1
  AMP PEAK 14(16P11.2) WILD-TYPE         23       28        13         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  STAGE I                              14                             60
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            29                            102
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              3
  STAGE IIIB                           20                             36
  STAGE IIIC                           16                             23
  STAGE IV                             15                             28
  STAGE IVA                             5                             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 14(16P11.2) MUTATED     3  19  89  11
  AMP PEAK 14(16P11.2) WILD-TYPE   8  59 212  41
D14V4, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  T1                            3                              8
  T2                           19                             59
  T3                           89                            212
  T4                           11                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 14(16P11.2) MUTATED    53  37  33
  AMP PEAK 14(16P11.2) WILD-TYPE 204  67  48
D14V5, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  N0                           53                            204
  N1                           37                             67
  N2                           33                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED    83  21
  AMP PEAK 14(16P11.2) WILD-TYPE 239  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED     83   21
  AMP PEAK 14(16P11.2) WILD-TYPE  239   41
   clus
vv  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  0                           83                            239
  1                           21                             41
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED    61  62
  AMP PEAK 14(16P11.2) WILD-TYPE 149 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED     61   62
  AMP PEAK 14(16P11.2) WILD-TYPE  149  171
        clus
vv       AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  FEMALE                           61                            149
  MALE                             62                            171
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED   114   8
  AMP PEAK 14(16P11.2) WILD-TYPE 267  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED    114    8
  AMP PEAK 14(16P11.2) WILD-TYPE  267   52
                               clus
vv                              AMP PEAK 14(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                   114
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              AMP PEAK 14(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     267
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED     1 122
  AMP PEAK 14(16P11.2) WILD-TYPE   2 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED      1  122
  AMP PEAK 14(16P11.2) WILD-TYPE    2  318
     clus
vv    AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  NO                             1                              2
  YES                          122                            318
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(16P11.2) MUTATED    93   0   7   5
  AMP PEAK 14(16P11.2) WILD-TYPE 223   3  17  20
D14V10, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  R0                           93                            223
  R1                            0                              3
  R2                            7                             17
  RX                            5                             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"
D14V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(16P11.2) MUTATED                                  1     3
  AMP PEAK 14(16P11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(16P11.2) MUTATED                          13    61
  AMP PEAK 14(16P11.2) WILD-TYPE                        41   150
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      61
                                  clus
vv                                 AMP PEAK 14(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       150
[1] 4 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(16Q12.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(16Q12.1) MUTATED    89  15
  AMP PEAK 15(16Q12.1) WILD-TYPE 248  78
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           104                            326 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                            15                             78 
$`AMP PEAK 15(16Q12.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        24.33        42.28        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-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       24.13        25.08        23.87        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3673 
       33.99        13.02        24.00        19.99        19.99        50.04 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.02        19.00        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3939 
       33.07         0.99        17.03        24.03        27.02        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 
       24.00        20.98        34.03        16.08        26.01        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-6196 
       40.96        22.42        27.42         0.20         0.95         0.20 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
       17.26        18.84         5.13        62.79        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        1.94         3.29         1.35       102.44        49.08        21.99 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 
       20.02         8.02        22.03        22.98        16.01        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 
       14.04        29.03        21.99        14.99        15.02        11.01 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       10.06        19.59        18.25         1.32        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F 
       12.49        10.13        13.41        11.38        38.20        35.97 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 
        8.61        13.38         1.55        82.39        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-NH-A6GB 
       45.11        39.42        35.93        26.43        13.78        15.65 
TCGA-NH-A6GC TCGA-QL-A97D 
       12.79         9.70 

$`AMP PEAK 15(16Q12.1) 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-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       42.90        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-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.16        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        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-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       29.00         0.99        14.01        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04        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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        31.07        53.00        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 
        2.01        33.01        26.01        24.00         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       21.99        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        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-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         5.79        10.88        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
        0.46         0.92        14.50        27.09        16.31        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82        17.85        19.33        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-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.26         0.33         0.10        17.56        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        29.06        30.08        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-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
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-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-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-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 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-G4-6298 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-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       53.62        51.75        36.72        36.00        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 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-A8F7 
       18.18        10.98        19.33        19.33         9.93        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 
       30.28        70.03 

  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                        21.990                         20.155 
[1] "0.2 - 102.4 (22.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.5"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(16Q12.1) MUTATED        14        1        3        22         1
  AMP PEAK 15(16Q12.1) WILD-TYPE      60        0       25       109         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(16Q12.1) MUTATED           0         5          9         20
  AMP PEAK 15(16Q12.1) WILD-TYPE         1        16          3         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(16Q12.1) MUTATED           14       11         4         1
  AMP PEAK 15(16Q12.1) WILD-TYPE         25       32        14         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  STAGE I                              14                             60
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            22                            109
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              3
  STAGE IIIB                           20                             36
  STAGE IIIC                           14                             25
  STAGE IV                             11                             32
  STAGE IVA                             4                             14
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(16Q12.1) MUTATED     3  19  75  11
  AMP PEAK 15(16Q12.1) WILD-TYPE   8  59 226  41
D15V4, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  T1                            3                              8
  T2                           19                             59
  T3                           75                            226
  T4                           11                             41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 15(16Q12.1) MUTATED    46  35  28
  AMP PEAK 15(16Q12.1) WILD-TYPE 211  69  53
D15V5, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  N0                           46                            211
  N1                           35                             69
  N2                           28                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED    74  16
  AMP PEAK 15(16Q12.1) WILD-TYPE 248  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED     74   16
  AMP PEAK 15(16Q12.1) WILD-TYPE  248   46
   clus
vv  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  0                           74                            248
  1                           16                             46
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED    55  54
  AMP PEAK 15(16Q12.1) WILD-TYPE 155 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED     55   54
  AMP PEAK 15(16Q12.1) WILD-TYPE  155  179
        clus
vv       AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  FEMALE                           55                            155
  MALE                             54                            179
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED   101   7
  AMP PEAK 15(16Q12.1) WILD-TYPE 280  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED    101    7
  AMP PEAK 15(16Q12.1) WILD-TYPE  280   53
                               clus
vv                              AMP PEAK 15(16Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   101
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 15(16Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     280
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED     1 108
  AMP PEAK 15(16Q12.1) WILD-TYPE   2 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED      1  108
  AMP PEAK 15(16Q12.1) WILD-TYPE    2  332
     clus
vv    AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  NO                             1                              2
  YES                          108                            332
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(16Q12.1) MUTATED    83   0   6   4
  AMP PEAK 15(16Q12.1) WILD-TYPE 233   3  18  21
D15V10, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  R0                           83                            233
  R1                            0                              3
  R2                            6                             18
  RX                            4                             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"
D15V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(16Q12.1) MUTATED                                  1     2
  AMP PEAK 15(16Q12.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(16Q12.1) MUTATED                          10    57
  AMP PEAK 15(16Q12.1) WILD-TYPE                        44   154
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(16Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 15(16Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       154
[1] 4 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(17P11.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(17P11.2) MUTATED    35   7
  AMP PEAK 16(17P11.2) WILD-TYPE 302  86
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            42                            388 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                             7                             86 
$`AMP PEAK 16(17P11.2) MUTATED`
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-A6-2680 TCGA-A6-2686 TCGA-A6-3810 
       11.47         4.80        11.47        35.11        37.02        36.53 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-A56B 
       31.63        30.44        32.71        29.16        25.08        56.25 
TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 
       15.02        35.05         1.02        36.95        17.03         0.99 
TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-AD-6888 
       12.99        34.03         2.01        13.05        34.06         4.21 
TCGA-AZ-5407 TCGA-AZ-6607 TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6678 
       61.41         3.19         1.35        29.06        14.04        11.01 
TCGA-D5-6537 TCGA-D5-6924 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28M 
        4.80        14.30         6.12        14.04       119.93        95.18 
TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6317 
        1.55        23.51        74.56        55.04        35.93        36.00 

$`AMP PEAK 16(17P11.2) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       43.76        46.65        43.76        43.43        42.90        24.33 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        45.60        13.94        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5660 
       37.25        34.65        14.53        32.45        32.91        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-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-3532 TCGA-AA-3534 TCGA-AA-3538 
        0.00        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-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-3692 
       47.01        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-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
        0.99        25.02        17.98        15.95        38.99        37.02 
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-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        50.99        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-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-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-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-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-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 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-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-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-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-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        98.24         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67        13.25         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       19.43       107.67        28.21         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       65.85        53.62        44.68        51.75        45.11        39.42 
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-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 
       31.30         9.70        30.28        70.03 

  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                          0.99                           0.00 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                        119.93                         140.38 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                        24.295                         20.235 
[1] "1.0 - 119.9 (24.3)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.3"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(17P11.2) MUTATED         6        0        1        15         0
  AMP PEAK 16(17P11.2) WILD-TYPE      68        1       27       116         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(17P11.2) MUTATED           1         1          1          8
  AMP PEAK 16(17P11.2) WILD-TYPE         0        20         11         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(17P11.2) MUTATED            4        5         2         0
  AMP PEAK 16(17P11.2) WILD-TYPE         35       38        16         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  STAGE I                               6                             68
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            15                            116
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             1                             20
  STAGE IIIA                            1                             11
  STAGE IIIB                            8                             48
  STAGE IIIC                            4                             35
  STAGE IV                              5                             38
  STAGE IVA                             2                             16
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(17P11.2) MUTATED     2   6  30   6
  AMP PEAK 16(17P11.2) WILD-TYPE   9  72 271  46
D16V4, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  T1                            2                              9
  T2                            6                             72
  T3                           30                            271
  T4                            6                             46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 16(17P11.2) MUTATED    23  11   9
  AMP PEAK 16(17P11.2) WILD-TYPE 234  93  72
D16V5, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  N0                           23                            234
  N1                           11                             93
  N2                            9                             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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED    31   7
  AMP PEAK 16(17P11.2) WILD-TYPE 291  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED     31    7
  AMP PEAK 16(17P11.2) WILD-TYPE  291   55
   clus
vv  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  0                           31                            291
  1                            7                             55
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED    19  25
  AMP PEAK 16(17P11.2) WILD-TYPE 191 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED     19   25
  AMP PEAK 16(17P11.2) WILD-TYPE  191  208
        clus
vv       AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  FEMALE                           19                            191
  MALE                             25                            208
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED    38   6
  AMP PEAK 16(17P11.2) WILD-TYPE 343  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED     38    6
  AMP PEAK 16(17P11.2) WILD-TYPE  343   54
                               clus
vv                              AMP PEAK 16(17P11.2) MUTATED
  COLON ADENOCARCINOMA                                    38
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 16(17P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     343
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED     0  44
  AMP PEAK 16(17P11.2) WILD-TYPE   3 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED      0   44
  AMP PEAK 16(17P11.2) WILD-TYPE    3  396
     clus
vv    AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  NO                             0                              3
  YES                           44                            396
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(17P11.2) MUTATED    32   0   2   1
  AMP PEAK 16(17P11.2) WILD-TYPE 284   3  22  24
D16V10, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  R0                           32                            284
  R1                            0                              3
  R2                            2                             22
  RX                            1                             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"
D16V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(17P11.2) MUTATED                                  1     1
  AMP PEAK 16(17P11.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(17P11.2) MUTATED                           7    22
  AMP PEAK 16(17P11.2) WILD-TYPE                        47   189
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      22
                                  clus
vv                                 AMP PEAK 16(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       189
[1] 4 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(17Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(17Q12) MUTATED    91  16
  AMP PEAK 17(17Q12) WILD-TYPE 246  77
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         107                          323 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                          16                           77 
$`AMP PEAK 17(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 
       15.65        13.05        29.46        32.98        30.28 

$`AMP PEAK 17(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 
       42.77         8.42        31.30         9.70        70.03 

  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                      130.65                       140.38 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                       23.01                        19.99 
[1] "0.0 - 130.7 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.5"
D17V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(17Q12) MUTATED        14        0        4        29         1
  AMP PEAK 17(17Q12) WILD-TYPE      60        1       24       102         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(17Q12) MUTATED           1         4          4         16
  AMP PEAK 17(17Q12) WILD-TYPE         0        17          8         40
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(17Q12) MUTATED           12       17         6         1
  AMP PEAK 17(17Q12) WILD-TYPE         27       26        12         1
D17V3, multiclass
            clus
vv           AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  STAGE I                            14                           60
  STAGE IA                            0                            1
  STAGE II                            4                           24
  STAGE IIA                          29                          102
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                           4                           17
  STAGE IIIA                          4                            8
  STAGE IIIB                         16                           40
  STAGE IIIC                         12                           27
  STAGE IV                           17                           26
  STAGE IVA                           6                           12
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(17Q12) MUTATED     5  14  82  11
  AMP PEAK 17(17Q12) WILD-TYPE   6  64 219  41
D17V4, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  T1                          5                            6
  T2                         14                           64
  T3                         82                          219
  T4                         11                           41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 17(17Q12) MUTATED    56  29  26
  AMP PEAK 17(17Q12) WILD-TYPE 201  75  55
D17V5, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  N0                         56                          201
  N1                         29                           75
  N2                         26                           55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    69  24
  AMP PEAK 17(17Q12) WILD-TYPE 253  38
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     69   24
  AMP PEAK 17(17Q12) WILD-TYPE  253   38
   clus
vv  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  0                         69                          253
  1                         24                           38
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    48  64
  AMP PEAK 17(17Q12) WILD-TYPE 162 169
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     48   64
  AMP PEAK 17(17Q12) WILD-TYPE  162  169
        clus
vv       AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  FEMALE                         48                          162
  MALE                           64                          169
[1] 2 2
[1] FALSE
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    99  12
  AMP PEAK 17(17Q12) WILD-TYPE 282  48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     99   12
  AMP PEAK 17(17Q12) WILD-TYPE  282   48
                               clus
vv                              AMP PEAK 17(17Q12) MUTATED
  COLON ADENOCARCINOMA                                  99
  COLON MUCINOUS ADENOCARCINOMA                         12
                               clus
vv                              AMP PEAK 17(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                   282
  COLON MUCINOUS ADENOCARCINOMA                           48
[1] 2 2
[1] FALSE
D17V9, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED     1 111
  AMP PEAK 17(17Q12) WILD-TYPE   2 329
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED      1  111
  AMP PEAK 17(17Q12) WILD-TYPE    2  329
     clus
vv    AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  NO                           1                            2
  YES                        111                          329
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(17Q12) MUTATED    76   1  10   4
  AMP PEAK 17(17Q12) WILD-TYPE 240   2  14  21
D17V10, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  R0                         76                          240
  R1                          1                            2
  R2                         10                           14
  RX                          4                           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"
D17V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(17Q12) MUTATED                                  1     3
  AMP PEAK 17(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q12) MUTATED                          16    52
  AMP PEAK 17(17Q12) WILD-TYPE                        38   159
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                16
  WHITE                                                    52
                                  clus
vv                                 AMP PEAK 17(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  38
  WHITE                                                     159
[1] 4 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(17Q24.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(17Q24.1) MUTATED    89  12
  AMP PEAK 18(17Q24.1) WILD-TYPE 248  81
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           101                            329 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                            12                             81 
$`AMP PEAK 18(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-3956 
       10.06        36.03         0.99        24.03        12.99        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
        2.01        21.99        50.99        13.05        34.06        27.02 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z 
       13.94        38.04        21.99        12.00         1.02        37.02 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 
        5.03         0.92        41.00         4.21         0.79        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 
       16.44        14.50        16.31        61.41        29.56         2.24 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        0.07       102.44         8.02        13.02        29.06        22.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 
       17.03        14.04        29.03        21.99        14.99        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 
       11.08        11.01        12.26        19.59        11.51         1.32 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 
       15.12         4.80        17.13        14.30        13.41       130.65 
TCGA-DM-A285 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        6.12        95.18        74.56        65.85        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 
       39.42        35.93        36.00        26.43        91.79        46.75 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL 
       15.65        13.05        29.46        32.98        30.28 

$`AMP PEAK 18(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-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        2.01        20.98        16.08        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
       35.01        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.96        39.98         2.01        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
       40.96         0.07        21.37        56.55         0.72         5.79 
TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       22.42        10.88         0.20         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-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-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56        40.34        70.16        15.62        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-4751 TCGA-CM-5348 
       20.02        37.02        25.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       15.02        12.00        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       45.40        13.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        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-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        44.68        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        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 
       42.77         8.42        31.30         9.70        70.03 

  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                         22.03                          19.99 
[1] "0.1 - 130.7 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "2.1"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(17Q24.1) MUTATED        16        0        4        27         1
  AMP PEAK 18(17Q24.1) WILD-TYPE      58        1       24       104         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(17Q24.1) MUTATED           1         4          4         17
  AMP PEAK 18(17Q24.1) WILD-TYPE         0        17          8         39
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(17Q24.1) MUTATED            9       12         5         1
  AMP PEAK 18(17Q24.1) WILD-TYPE         30       31        13         1
D18V3, multiclass
            clus
vv           AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  STAGE I                              16                             58
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            27                            104
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            4                              8
  STAGE IIIB                           17                             39
  STAGE IIIC                            9                             30
  STAGE IV                             12                             31
  STAGE IVA                             5                             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 18(17Q24.1) MUTATED     4  17  75   8
  AMP PEAK 18(17Q24.1) WILD-TYPE   7  61 226  44
D18V4, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  T1                            4                              7
  T2                           17                             61
  T3                           75                            226
  T4                            8                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 18(17Q24.1) MUTATED    57  29  17
  AMP PEAK 18(17Q24.1) WILD-TYPE 200  75  64
D18V5, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  N0                           57                            200
  N1                           29                             75
  N2                           17                             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    68  18
  AMP PEAK 18(17Q24.1) WILD-TYPE 254  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     68   18
  AMP PEAK 18(17Q24.1) WILD-TYPE  254   44
   clus
vv  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  0                           68                            254
  1                           18                             44
[1] 2 2
[1] FALSE
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    52  52
  AMP PEAK 18(17Q24.1) WILD-TYPE 158 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     52   52
  AMP PEAK 18(17Q24.1) WILD-TYPE  158  181
        clus
vv       AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  FEMALE                           52                            158
  MALE                             52                            181
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    94   9
  AMP PEAK 18(17Q24.1) WILD-TYPE 287  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     94    9
  AMP PEAK 18(17Q24.1) WILD-TYPE  287   51
                               clus
vv                              AMP PEAK 18(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                    94
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              AMP PEAK 18(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     287
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED     1 103
  AMP PEAK 18(17Q24.1) WILD-TYPE   2 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED      1  103
  AMP PEAK 18(17Q24.1) WILD-TYPE    2  337
     clus
vv    AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  NO                             1                              2
  YES                          103                            337
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(17Q24.1) MUTATED    75   1   8   3
  AMP PEAK 18(17Q24.1) WILD-TYPE 241   2  16  22
D18V10, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  R0                           75                            241
  R1                            1                              2
  R2                            8                             16
  RX                            3                             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"
D18V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(17Q24.1) MUTATED                                  0     2
  AMP PEAK 18(17Q24.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17Q24.1) MUTATED                          15    51
  AMP PEAK 18(17Q24.1) WILD-TYPE                        39   160
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      51
                                  clus
vv                                 AMP PEAK 18(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    39
  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(19) Variable = AMP PEAK 19(19P13.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(19P13.2) MUTATED    57  14
  AMP PEAK 19(19P13.2) WILD-TYPE 280  79
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            71                            359 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            14                             79 
$`AMP PEAK 19(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 
       26.43        47.15        13.05        29.46         9.70 

$`AMP PEAK 19(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 
       32.98         8.42        31.30        30.28        70.03 

  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                          0.46                           0.00 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                         74.56                         140.38 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                         21.99                          20.19 
[1] "0.5 - 74.6 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(19P13.2) MUTATED        10        0        4        20         1
  AMP PEAK 19(19P13.2) WILD-TYPE      64        1       24       111         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(19P13.2) MUTATED           0         5          3         13
  AMP PEAK 19(19P13.2) WILD-TYPE         1        16          9         43
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(19P13.2) MUTATED            5        7         5         0
  AMP PEAK 19(19P13.2) WILD-TYPE         34       36        13         2
D19V3, multiclass
            clus
vv           AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            20                            111
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            3                              9
  STAGE IIIB                           13                             43
  STAGE IIIC                            5                             34
  STAGE IV                              7                             36
  STAGE IVA                             5                             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 19(19P13.2) MUTATED     2  10  55   8
  AMP PEAK 19(19P13.2) WILD-TYPE   9  68 246  44
D19V4, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  T1                            2                              9
  T2                           10                             68
  T3                           55                            246
  T4                            8                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 19(19P13.2) MUTATED    38  26  11
  AMP PEAK 19(19P13.2) WILD-TYPE 219  78  70
D19V5, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  N0                           38                            219
  N1                           26                             78
  N2                           11                             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"
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    45  12
  AMP PEAK 19(19P13.2) WILD-TYPE 277  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     45   12
  AMP PEAK 19(19P13.2) WILD-TYPE  277   50
   clus
vv  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  0                           45                            277
  1                           12                             50
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    29  46
  AMP PEAK 19(19P13.2) WILD-TYPE 181 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     29   46
  AMP PEAK 19(19P13.2) WILD-TYPE  181  187
        clus
vv       AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  FEMALE                           29                            181
  MALE                             46                            187
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    67   8
  AMP PEAK 19(19P13.2) WILD-TYPE 314  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     67    8
  AMP PEAK 19(19P13.2) WILD-TYPE  314   52
                               clus
vv                              AMP PEAK 19(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                    67
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              AMP PEAK 19(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     314
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED     1  74
  AMP PEAK 19(19P13.2) WILD-TYPE   2 366
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED      1   74
  AMP PEAK 19(19P13.2) WILD-TYPE    2  366
     clus
vv    AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  NO                             1                              2
  YES                           74                            366
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(19P13.2) MUTATED    52   2   3   6
  AMP PEAK 19(19P13.2) WILD-TYPE 264   1  21  19
D19V10, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  R0                           52                            264
  R1                            2                              1
  R2                            3                             21
  RX                            6                             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"
D19V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(19P13.2) MUTATED                                  0     2
  AMP PEAK 19(19P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(19P13.2) MUTATED                          13    42
  AMP PEAK 19(19P13.2) WILD-TYPE                        41   169
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      42
                                  clus
vv                                 AMP PEAK 19(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       169
[1] 4 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(19Q13.11) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(19Q13.11) MUTATED    73  16
  AMP PEAK 20(19Q13.11) WILD-TYPE 264  77
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             89                             341 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             16                              77 
$`AMP PEAK 20(19Q13.11) 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-3522 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 
       35.01        58.03        37.05        12.99        13.02        37.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 
       35.05         0.99        37.02        33.07        36.03        12.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z 
       50.99        13.05        18.05        27.02        42.02        21.99 
TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 TCGA-AD-6899 
       12.00        51.98        39.98         0.92         4.21         5.79 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       22.42        16.44        14.50         0.20        17.85        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-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       21.99         2.01        37.02        25.02        13.02        29.06 
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-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 
       13.64        35.41        82.39        74.56        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 TCGA-QG-A5YW TCGA-QL-A97D 
       26.43        47.15        13.05        29.46         9.70 

$`AMP PEAK 20(19Q13.11) 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-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-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-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-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        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-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05        38.04         4.01         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        32.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        26.01        37.02        39.06         2.96         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-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-A71X 
        0.95        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-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-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 
       20.02        26.04         8.02        27.02        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-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67        13.25         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21         8.35        23.51        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-G4-6321 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-G4-6626 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 
       32.98         8.42        31.30        30.28        70.03 

  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                            0.2                             0.0 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                          21.99                           20.02 
[1] "0.2 - 119.7 (22.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(19Q13.11) MUTATED        13        0        4        29         0
  AMP PEAK 20(19Q13.11) WILD-TYPE      61        1       24       102         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(19Q13.11) MUTATED           0         3          4         14
  AMP PEAK 20(19Q13.11) WILD-TYPE         1        18          8         42
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(19Q13.11) MUTATED            9       11         5         0
  AMP PEAK 20(19Q13.11) WILD-TYPE         30       32        13         2
D20V3, multiclass
            clus
vv           AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  STAGE I                               13                              61
  STAGE IA                               0                               1
  STAGE II                               4                              24
  STAGE IIA                             29                             102
  STAGE IIB                              0                               8
  STAGE IIC                              0                               1
  STAGE III                              3                              18
  STAGE IIIA                             4                               8
  STAGE IIIB                            14                              42
  STAGE IIIC                             9                              30
  STAGE IV                              11                              32
  STAGE IVA                              5                              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 20(19Q13.11) MUTATED     2  15  69   8
  AMP PEAK 20(19Q13.11) WILD-TYPE   9  63 232  44
D20V4, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  T1                             2                               9
  T2                            15                              63
  T3                            69                             232
  T4                             8                              44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 20(19Q13.11) MUTATED    49  29  15
  AMP PEAK 20(19Q13.11) WILD-TYPE 208  75  66
D20V5, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  N0                            49                             208
  N1                            29                              75
  N2                            15                              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"
D20V6, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED    60  16
  AMP PEAK 20(19Q13.11) WILD-TYPE 262  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED     60   16
  AMP PEAK 20(19Q13.11) WILD-TYPE  262   46
   clus
vv  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  0                            60                             262
  1                            16                              46
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED    38  56
  AMP PEAK 20(19Q13.11) WILD-TYPE 172 177
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED     38   56
  AMP PEAK 20(19Q13.11) WILD-TYPE  172  177
        clus
vv       AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  FEMALE                            38                             172
  MALE                              56                             177
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED    83  11
  AMP PEAK 20(19Q13.11) WILD-TYPE 298  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED     83   11
  AMP PEAK 20(19Q13.11) WILD-TYPE  298   49
                               clus
vv                              AMP PEAK 20(19Q13.11) MUTATED
  COLON ADENOCARCINOMA                                     83
  COLON MUCINOUS ADENOCARCINOMA                            11
                               clus
vv                              AMP PEAK 20(19Q13.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      298
  COLON MUCINOUS ADENOCARCINOMA                              49
[1] 2 2
[1] FALSE
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED     1  93
  AMP PEAK 20(19Q13.11) WILD-TYPE   2 347
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED      1   93
  AMP PEAK 20(19Q13.11) WILD-TYPE    2  347
     clus
vv    AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  NO                              1                               2
  YES                            93                             347
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(19Q13.11) MUTATED    69   1   4   6
  AMP PEAK 20(19Q13.11) WILD-TYPE 247   2  20  19
D20V10, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  R0                            69                             247
  R1                             1                               2
  R2                             4                              20
  RX                             6                              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"
D20V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(19Q13.11) MUTATED                                  0     2
  AMP PEAK 20(19Q13.11) WILD-TYPE                                1     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19Q13.11) MUTATED                          14    52
  AMP PEAK 20(19Q13.11) WILD-TYPE                        40   159
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 20(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     40
  WHITE                                                        159
[1] 4 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(20P12.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(20P12.1) MUTATED   152  48
  AMP PEAK 21(20P12.1) WILD-TYPE 185  45
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           200                            230 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                            48                             45 
$`AMP PEAK 21(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-A6-5659 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6649 
       36.53        32.45        30.44        27.09        25.08        24.16 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.69        20.28        61.84         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3530 
        1.02        58.03         6.97         1.02         0.00        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 
       29.00        29.00        14.01        21.01        13.02        23.01 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        19.99         6.05         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.05        15.02        37.05        19.00        36.00         5.03 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       10.06         0.99        38.99        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 
       27.02        18.05        12.99        24.00        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K 
       24.00        27.02        19.07         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C 
       38.04         4.01        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       10.98        12.00        31.00        33.04        26.01        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        41.00        39.98 
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-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L 
       27.42        16.44        14.50        16.31         0.95        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
       17.85        19.33        18.84         1.41         5.13        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 
       65.00        62.79        49.41        12.10        29.56         3.19 
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-4950 TCGA-CK-5912 TCGA-CM-4744 TCGA-CM-4747 
        1.35        17.56        40.34        49.08        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
        8.02        13.02        29.06        22.98         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        16.04        21.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       14.04        11.01        11.08        11.01        45.40        12.26 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       19.59        20.19        17.75        17.85        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       12.39        10.13        12.43         9.04        11.64        13.41 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26       119.70        24.43        12.59         7.50        44.32 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      139.17         6.12        14.04        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 
        8.61        13.38        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 
       29.46        32.98 

$`AMP PEAK 21(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-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.25        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       24.13         8.38        25.18        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        56.25 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 
        3.02        37.05         1.02        35.01        63.98        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-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        34.03        26.01        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       33.99        24.00        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       61.02        78.08         6.97        54.02         0.92        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98        85.05        26.99        19.04        19.04 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
       35.05        25.02         1.02        17.98        15.95        36.95 
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-3867 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       24.03        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       24.00         2.01        20.98        25.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
        0.99        34.98        15.02        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 
       39.98        22.03        18.05        40.96         4.21        56.55 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
       10.88         0.20         0.46         0.92        27.09        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        0.20        21.44        17.82        75.25        50.37        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
        5.65        32.94        22.36        61.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
        5.23        11.74         1.94         3.25         0.33         0.10 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 
       27.02        22.03        30.08        16.01        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 
       29.03        14.99        12.99        13.02        15.02        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       13.05        11.08        10.06        12.03        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.42        18.25         1.32        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 
       17.13        16.14        15.58        14.30         9.44         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.00        11.38        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A 
       13.32       140.38       131.51       135.65         7.76        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 
       81.37       119.93        60.79        98.24        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 
       30.28        70.03 

  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                             0                              0 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                        139.17                         140.38 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                         17.80                          23.28 
[1] "0.0 - 139.2 (17.8)" "0.0 - 140.4 (23.3)"
[1] "hr=" "1.5"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20P12.1) MUTATED        38        1       10        53         3
  AMP PEAK 21(20P12.1) WILD-TYPE      36        0       18        78         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20P12.1) MUTATED           0         8         10         18
  AMP PEAK 21(20P12.1) WILD-TYPE         1        13          2         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(20P12.1) MUTATED           17       31        10         1
  AMP PEAK 21(20P12.1) WILD-TYPE         22       12         8         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  STAGE I                              38                             36
  STAGE IA                              1                              0
  STAGE II                             10                             18
  STAGE IIA                            53                             78
  STAGE IIB                             3                              5
  STAGE IIC                             0                              1
  STAGE III                             8                             13
  STAGE IIIA                           10                              2
  STAGE IIIB                           18                             38
  STAGE IIIC                           17                             22
  STAGE IV                             31                             12
  STAGE IVA                            10                              8
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(20P12.1) MUTATED     6  40 136  23
  AMP PEAK 21(20P12.1) WILD-TYPE   5  38 165  29
D21V4, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  T1                            6                              5
  T2                           40                             38
  T3                          136                            165
  T4                           23                             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 21(20P12.1) MUTATED   112  54  40
  AMP PEAK 21(20P12.1) WILD-TYPE 145  50  41
D21V5, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  N0                          112                            145
  N1                           54                             50
  N2                           40                             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"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED   136  41
  AMP PEAK 21(20P12.1) WILD-TYPE 186  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED    136   41
  AMP PEAK 21(20P12.1) WILD-TYPE  186   21
   clus
vv  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  0                          136                            186
  1                           41                             21
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED    91 115
  AMP PEAK 21(20P12.1) WILD-TYPE 119 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED     91  115
  AMP PEAK 21(20P12.1) WILD-TYPE  119  118
        clus
vv       AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  FEMALE                           91                            119
  MALE                            115                            118
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED   184  20
  AMP PEAK 21(20P12.1) WILD-TYPE 197  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED    184   20
  AMP PEAK 21(20P12.1) WILD-TYPE  197   40
                               clus
vv                              AMP PEAK 21(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                   184
  COLON MUCINOUS ADENOCARCINOMA                           20
                               clus
vv                              AMP PEAK 21(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     197
  COLON MUCINOUS ADENOCARCINOMA                             40
[1] 2 2
[1] FALSE
D21V9, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED     3 203
  AMP PEAK 21(20P12.1) WILD-TYPE   0 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED      3  203
  AMP PEAK 21(20P12.1) WILD-TYPE    0  237
     clus
vv    AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  NO                             3                              0
  YES                          203                            237
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(20P12.1) MUTATED   143   2  18  11
  AMP PEAK 21(20P12.1) WILD-TYPE 173   1   6  14
D21V10, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  R0                          143                            173
  R1                            2                              1
  R2                           18                              6
  RX                           11                             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"
D21V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(20P12.1) MUTATED                                  1     7
  AMP PEAK 21(20P12.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20P12.1) MUTATED                          23    96
  AMP PEAK 21(20P12.1) WILD-TYPE                        31   115
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK 21(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    31
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(20P11.21) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20P11.21) MUTATED   186  54
  AMP PEAK 22(20P11.21) WILD-TYPE 151  39
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            240                             190 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                             54                              39 
$`AMP PEAK 22(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 

$`AMP PEAK 22(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 
       12.00        31.30        30.28        70.03 

  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                         18.215                          23.330 
[1] "0.0 - 139.2 (18.2)" "0.0 - 140.4 (23.3)"
[1] "hr=" "1.2"
D22V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20P11.21) MUTATED        43        1       14        65         3
  AMP PEAK 22(20P11.21) WILD-TYPE      31        0       14        66         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20P11.21) MUTATED           0         9         11         26
  AMP PEAK 22(20P11.21) WILD-TYPE         1        12          1         30
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20P11.21) MUTATED           21       35        12         1
  AMP PEAK 22(20P11.21) WILD-TYPE         18        8         6         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  STAGE I                               43                              31
  STAGE IA                               1                               0
  STAGE II                              14                              14
  STAGE IIA                             65                              66
  STAGE IIB                              3                               5
  STAGE IIC                              0                               1
  STAGE III                              9                              12
  STAGE IIIA                            11                               1
  STAGE IIIB                            26                              30
  STAGE IIIC                            21                              18
  STAGE IV                              35                               8
  STAGE IVA                             12                               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 22(20P11.21) MUTATED     7  47 166  27
  AMP PEAK 22(20P11.21) WILD-TYPE   4  31 135  25
D22V4, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  T1                             7                               4
  T2                            47                              31
  T3                           166                             135
  T4                            27                              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
  AMP PEAK 22(20P11.21) MUTATED   136  66  46
  AMP PEAK 22(20P11.21) WILD-TYPE 121  38  35
D22V5, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  N0                           136                             121
  N1                            66                              38
  N2                            46                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED   166  47
  AMP PEAK 22(20P11.21) WILD-TYPE 156  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED    166   47
  AMP PEAK 22(20P11.21) WILD-TYPE  156   15
   clus
vv  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  0                           166                             156
  1                            47                              15
[1] 2 2
[1] FALSE
D22V7, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED   112 136
  AMP PEAK 22(20P11.21) WILD-TYPE  98  97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED    112  136
  AMP PEAK 22(20P11.21) WILD-TYPE   98   97
        clus
vv       AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  FEMALE                           112                              98
  MALE                             136                              97
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED   224  22
  AMP PEAK 22(20P11.21) WILD-TYPE 157  38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED    224   22
  AMP PEAK 22(20P11.21) WILD-TYPE  157   38
                               clus
vv                              AMP PEAK 22(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                    224
  COLON MUCINOUS ADENOCARCINOMA                            22
                               clus
vv                              AMP PEAK 22(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      157
  COLON MUCINOUS ADENOCARCINOMA                              38
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED     3 245
  AMP PEAK 22(20P11.21) WILD-TYPE   0 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED      3  245
  AMP PEAK 22(20P11.21) WILD-TYPE    0  195
     clus
vv    AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  NO                              3                               0
  YES                           245                             195
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20P11.21) MUTATED   170   2  20  12
  AMP PEAK 22(20P11.21) WILD-TYPE 146   1   4  13
D22V10, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  R0                           170                             146
  R1                             2                               1
  R2                            20                               4
  RX                            12                              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"
D22V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20P11.21) MUTATED                                  1     7
  AMP PEAK 22(20P11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20P11.21) MUTATED                          28   121
  AMP PEAK 22(20P11.21) WILD-TYPE                        26    90
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      121
                                  clus
vv                                 AMP PEAK 22(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                         90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(20Q11.21) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20Q11.21) MUTATED   244  64
  AMP PEAK 23(20Q11.21) WILD-TYPE  93  29
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            308                             122 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             64                              29 
$`AMP PEAK 23(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 
        9.70        30.28 

$`AMP PEAK 23(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 
       31.30        70.03 

  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                          19.46                           22.09 
[1] "0.0 - 139.2 (19.5)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q11.21) MUTATED        53        1       16        84         3
  AMP PEAK 23(20Q11.21) WILD-TYPE      21        0       12        47         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q11.21) MUTATED           1        14         12         40
  AMP PEAK 23(20Q11.21) WILD-TYPE         0         7          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20Q11.21) MUTATED           31       38        16         1
  AMP PEAK 23(20Q11.21) WILD-TYPE          8        5         2         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  STAGE I                               53                              21
  STAGE IA                               1                               0
  STAGE II                              16                              12
  STAGE IIA                             84                              47
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             14                               7
  STAGE IIIA                            12                               0
  STAGE IIIB                            40                              16
  STAGE IIIC                            31                               8
  STAGE IV                              38                               5
  STAGE IVA                             16                               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 23(20Q11.21) MUTATED     7  59 218  32
  AMP PEAK 23(20Q11.21) WILD-TYPE   4  19  83  20
D23V4, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  T1                             7                               4
  T2                            59                              19
  T3                           218                              83
  T4                            32                              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 23(20Q11.21) MUTATED   169  84  63
  AMP PEAK 23(20Q11.21) WILD-TYPE  88  20  18
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  N0                           169                              88
  N1                            84                              20
  N2                            63                              18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED   222  54
  AMP PEAK 23(20Q11.21) WILD-TYPE 100   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED    222   54
  AMP PEAK 23(20Q11.21) WILD-TYPE  100    8
   clus
vv  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  0                           222                             100
  1                            54                               8
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED   145 172
  AMP PEAK 23(20Q11.21) WILD-TYPE  65  61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED    145  172
  AMP PEAK 23(20Q11.21) WILD-TYPE   65   61
        clus
vv       AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  FEMALE                           145                              65
  MALE                             172                              61
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED   289  26
  AMP PEAK 23(20Q11.21) WILD-TYPE  92  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED    289   26
  AMP PEAK 23(20Q11.21) WILD-TYPE   92   34
                               clus
vv                              AMP PEAK 23(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                    289
  COLON MUCINOUS ADENOCARCINOMA                            26
                               clus
vv                              AMP PEAK 23(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       92
  COLON MUCINOUS ADENOCARCINOMA                              34
[1] 2 2
[1] FALSE
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED     3 314
  AMP PEAK 23(20Q11.21) WILD-TYPE   0 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED      3  314
  AMP PEAK 23(20Q11.21) WILD-TYPE    0  126
     clus
vv    AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  NO                              3                               0
  YES                           314                             126
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20Q11.21) MUTATED   224   2  21  14
  AMP PEAK 23(20Q11.21) WILD-TYPE  92   1   3  11
D23V10, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  R0                           224                              92
  R1                             2                               1
  R2                            21                               3
  RX                            14                              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"
D23V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(20Q11.21) MUTATED                                  1     7
  AMP PEAK 23(20Q11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20Q11.21) MUTATED                          38   154
  AMP PEAK 23(20Q11.21) WILD-TYPE                        16    57
D23V12, multiclass
                                  clus
vv                                 AMP PEAK 23(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      154
                                  clus
vv                                 AMP PEAK 23(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                         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"

Clustering(24) Variable = AMP PEAK 24(20Q12) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(20Q12) MUTATED   245  64
  AMP PEAK 24(20Q12) WILD-TYPE  92  29
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         309                          121 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                          64                           29 
$`AMP PEAK 24(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 
        8.42         9.70        30.28 

$`AMP PEAK 24(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 
       70.03 

  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                      139.17                       140.38 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                       19.59                        22.09 
[1] "0.0 - 139.2 (19.6)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D24V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 24(20Q12) MUTATED        53        1       16        85         3
  AMP PEAK 24(20Q12) WILD-TYPE      21        0       12        46         5
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(20Q12) MUTATED           1        13         12         40
  AMP PEAK 24(20Q12) WILD-TYPE         0         8          0         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20Q12) MUTATED           31       38        17         1
  AMP PEAK 24(20Q12) WILD-TYPE          8        5         1         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  STAGE I                            53                           21
  STAGE IA                            1                            0
  STAGE II                           16                           12
  STAGE IIA                          85                           46
  STAGE IIB                           3                            5
  STAGE IIC                           1                            0
  STAGE III                          13                            8
  STAGE IIIA                         12                            0
  STAGE IIIB                         40                           16
  STAGE IIIC                         31                            8
  STAGE IV                           38                            5
  STAGE IVA                          17                            1
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 24(20Q12) MUTATED     7  59 218  33
  AMP PEAK 24(20Q12) WILD-TYPE   4  19  83  19
D24V4, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  T1                          7                            4
  T2                         59                           19
  T3                        218                           83
  T4                         33                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 24(20Q12) MUTATED   170  84  63
  AMP PEAK 24(20Q12) WILD-TYPE  87  20  18
D24V5, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  N0                        170                           87
  N1                         84                           20
  N2                         63                           18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED   222  55
  AMP PEAK 24(20Q12) WILD-TYPE 100   7
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED    222   55
  AMP PEAK 24(20Q12) WILD-TYPE  100    7
   clus
vv  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  0                        222                          100
  1                         55                            7
[1] 2 2
[1] FALSE
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED   145 173
  AMP PEAK 24(20Q12) WILD-TYPE  65  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED    145  173
  AMP PEAK 24(20Q12) WILD-TYPE   65   60
        clus
vv       AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  FEMALE                        145                           65
  MALE                          173                           60
[1] 2 2
[1] FALSE
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED   291  25
  AMP PEAK 24(20Q12) WILD-TYPE  90  35
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED    291   25
  AMP PEAK 24(20Q12) WILD-TYPE   90   35
                               clus
vv                              AMP PEAK 24(20Q12) MUTATED
  COLON ADENOCARCINOMA                                 291
  COLON MUCINOUS ADENOCARCINOMA                         25
                               clus
vv                              AMP PEAK 24(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                           35
[1] 2 2
[1] FALSE
D24V9, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED     3 315
  AMP PEAK 24(20Q12) WILD-TYPE   0 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED      3  315
  AMP PEAK 24(20Q12) WILD-TYPE    0  125
     clus
vv    AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  NO                           3                            0
  YES                        315                          125
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 24(20Q12) MUTATED   225   2  21  14
  AMP PEAK 24(20Q12) WILD-TYPE  91   1   3  11
D24V10, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  R0                        225                           91
  R1                          2                            1
  R2                         21                            3
  RX                         14                           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"
D24V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(20Q12) MUTATED                                  1     7
  AMP PEAK 24(20Q12) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(20Q12) MUTATED                          38   157
  AMP PEAK 24(20Q12) WILD-TYPE                        16    54
D24V12, multiclass
                                  clus
vv                                 AMP PEAK 24(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                38
  WHITE                                                   157
                                  clus
vv                                 AMP PEAK 24(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      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"

Clustering(25) Variable = AMP PEAK 25(20Q13.12) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(20Q13.12) MUTATED   245  66
  AMP PEAK 25(20Q13.12) WILD-TYPE  92  27
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            311                             119 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                             66                              27 
$`AMP PEAK 25(20Q13.12) 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-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        15.02        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-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        17.85        18.84        75.25         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-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 
       29.46        32.98         8.42         9.70        30.28 

$`AMP PEAK 25(20Q13.12) 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-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
        5.98        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-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
       21.44        17.82        19.33        50.37        58.39        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 
       10.98        19.33         9.93        31.30        70.03 

  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                              0                               0 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                          19.59                           22.09 
[1] "0.0 - 139.2 (19.6)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D25V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 25(20Q13.12) MUTATED        52        1       17        85         3
  AMP PEAK 25(20Q13.12) WILD-TYPE      22        0       11        46         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(20Q13.12) MUTATED           1        13         12         40
  AMP PEAK 25(20Q13.12) WILD-TYPE         0         8          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(20Q13.12) MUTATED           32       39        17         1
  AMP PEAK 25(20Q13.12) WILD-TYPE          7        4         1         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  STAGE I                               52                              22
  STAGE IA                               1                               0
  STAGE II                              17                              11
  STAGE IIA                             85                              46
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             13                               8
  STAGE IIIA                            12                               0
  STAGE IIIB                            40                              16
  STAGE IIIC                            32                               7
  STAGE IV                              39                               4
  STAGE IVA                             17                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(20Q13.12) MUTATED     7  58 220  34
  AMP PEAK 25(20Q13.12) WILD-TYPE   4  20  81  18
D25V4, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  T1                             7                               4
  T2                            58                              20
  T3                           220                              81
  T4                            34                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 25(20Q13.12) MUTATED   170  84  65
  AMP PEAK 25(20Q13.12) WILD-TYPE  87  20  16
D25V5, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  N0                           170                              87
  N1                            84                              20
  N2                            65                              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED   223  56
  AMP PEAK 25(20Q13.12) WILD-TYPE  99   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED    223   56
  AMP PEAK 25(20Q13.12) WILD-TYPE   99    6
   clus
vv  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  0                           223                              99
  1                            56                               6
[1] 2 2
[1] FALSE
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED   146 174
  AMP PEAK 25(20Q13.12) WILD-TYPE  64  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED    146  174
  AMP PEAK 25(20Q13.12) WILD-TYPE   64   59
        clus
vv       AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  FEMALE                           146                              64
  MALE                             174                              59
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED   292  26
  AMP PEAK 25(20Q13.12) WILD-TYPE  89  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED    292   26
  AMP PEAK 25(20Q13.12) WILD-TYPE   89   34
                               clus
vv                              AMP PEAK 25(20Q13.12) MUTATED
  COLON ADENOCARCINOMA                                    292
  COLON MUCINOUS ADENOCARCINOMA                            26
                               clus
vv                              AMP PEAK 25(20Q13.12) WILD-TYPE
  COLON ADENOCARCINOMA                                       89
  COLON MUCINOUS ADENOCARCINOMA                              34
[1] 2 2
[1] FALSE
D25V9, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED     3 317
  AMP PEAK 25(20Q13.12) WILD-TYPE   0 123
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED      3  317
  AMP PEAK 25(20Q13.12) WILD-TYPE    0  123
     clus
vv    AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  NO                              3                               0
  YES                           317                             123
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 25(20Q13.12) MUTATED   226   2  21  14
  AMP PEAK 25(20Q13.12) WILD-TYPE  90   1   3  11
D25V10, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  R0                           226                              90
  R1                             2                               1
  R2                            21                               3
  RX                            14                              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"
D25V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(20Q13.12) MUTATED                                  1     7
  AMP PEAK 25(20Q13.12) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(20Q13.12) MUTATED                          37   158
  AMP PEAK 25(20Q13.12) WILD-TYPE                        17    53
D25V12, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      158
                                  clus
vv                                 AMP PEAK 25(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                         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"

Clustering(26) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   118  41
  DEL PEAK  1(1P36.11) WILD-TYPE 219  52
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           159                            271 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            41                             52 
$`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 
        9.93        12.00        42.77 

$`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 
       70.03 

  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 
                         19.07                          20.98 
[1] "0.1 - 139.2 (19.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.11) MUTATED        21        0        5        45         1
  DEL PEAK  1(1P36.11) WILD-TYPE      53        1       23        86         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1         8          4         19
  DEL PEAK  1(1P36.11) WILD-TYPE         0        13          8         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           17       29        10         0
  DEL PEAK  1(1P36.11) WILD-TYPE         22       14         8         2
D26V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              21                             53
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            45                             86
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            4                              8
  STAGE IIIB                           19                             37
  STAGE IIIC                           17                             22
  STAGE IV                             29                             14
  STAGE IVA                            10                              8
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED     3  26 113  22
  DEL PEAK  1(1P36.11) WILD-TYPE   8  52 188  30
D26V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            3                              8
  T2                           26                             52
  T3                          113                            188
  T4                           22                             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  1(1P36.11) MUTATED    81  43  40
  DEL PEAK  1(1P36.11) WILD-TYPE 176  61  41
D26V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           81                            176
  N1                           43                             61
  N2                           40                             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"
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   106  39
  DEL PEAK  1(1P36.11) WILD-TYPE 216  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    106   39
  DEL PEAK  1(1P36.11) WILD-TYPE  216   23
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          106                            216
  1                           39                             23
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    70  94
  DEL PEAK  1(1P36.11) WILD-TYPE 140 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     70   94
  DEL PEAK  1(1P36.11) WILD-TYPE  140  139
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           70                            140
  MALE                             94                            139
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   152  11
  DEL PEAK  1(1P36.11) WILD-TYPE 229  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    152   11
  DEL PEAK  1(1P36.11) WILD-TYPE  229   49
                               clus
vv                              DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                   152
  COLON MUCINOUS ADENOCARCINOMA                           11
                               clus
vv                              DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                     229
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D26V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     1 163
  DEL PEAK  1(1P36.11) WILD-TYPE   2 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      1  163
  DEL PEAK  1(1P36.11) WILD-TYPE    2  277
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             1                              2
  YES                          163                            277
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   109   1  14  11
  DEL PEAK  1(1P36.11) WILD-TYPE 207   2  10  14
D26V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          109                            207
  R1                            1                              2
  R2                           14                             10
  RX                           11                             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"
D26V11, 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     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                          16    79
  DEL PEAK  1(1P36.11) WILD-TYPE                        38   132
D26V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       132
[1] 4 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 = DEL PEAK  2(1P33) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED    82  34
  DEL PEAK  2(1P33) WILD-TYPE 255  59
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        116                         314 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         34                          59 
$`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 
       12.00        42.77 

$`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 
       30.28        70.03 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          0                           0 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      92.75                      140.38 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      17.85                       21.06 
[1] "0.0 - 92.8 (17.9)"  "0.0 - 140.4 (21.1)"
[1] "hr=" "1.9"
D27V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  2(1P33) MUTATED        12        0        5        34         0
  DEL PEAK  2(1P33) WILD-TYPE      62        1       23        97         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         6          3         16
  DEL PEAK  2(1P33) WILD-TYPE         1        15          9         40
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           14       22         4         0
  DEL PEAK  2(1P33) WILD-TYPE         25       21        14         2
D27V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           12                          62
  STAGE IA                           0                           1
  STAGE II                           5                          23
  STAGE IIA                         34                          97
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          6                          15
  STAGE IIIA                         3                           9
  STAGE IIIB                        16                          40
  STAGE IIIC                        14                          25
  STAGE IV                          22                          21
  STAGE IVA                          4                          14
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  2(1P33) MUTATED     3  15  85  17
  DEL PEAK  2(1P33) WILD-TYPE   8  63 216  35
D27V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         3                           8
  T2                        15                          63
  T3                        85                         216
  T4                        17                          35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK  2(1P33) MUTATED    57  33  30
  DEL PEAK  2(1P33) WILD-TYPE 200  71  51
D27V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        57                         200
  N1                        33                          71
  N2                        30                          51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    77  26
  DEL PEAK  2(1P33) WILD-TYPE 245  36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     77   26
  DEL PEAK  2(1P33) WILD-TYPE  245   36
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                        77                         245
  1                        26                          36
[1] 2 2
[1] FALSE
D27V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    53  67
  DEL PEAK  2(1P33) WILD-TYPE 157 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     53   67
  DEL PEAK  2(1P33) WILD-TYPE  157  166
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        53                         157
  MALE                          67                         166
[1] 2 2
[1] FALSE
D27V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   110  10
  DEL PEAK  2(1P33) WILD-TYPE 271  50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    110   10
  DEL PEAK  2(1P33) WILD-TYPE  271   50
                               clus
vv                              DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                110
  COLON MUCINOUS ADENOCARCINOMA                        10
                               clus
vv                              DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                  271
  COLON MUCINOUS ADENOCARCINOMA                          50
[1] 2 2
[1] FALSE
D27V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     0 120
  DEL PEAK  2(1P33) WILD-TYPE   3 320
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      0  120
  DEL PEAK  2(1P33) WILD-TYPE    3  320
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          0                           3
  YES                       120                         320
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED    78   1  10   7
  DEL PEAK  2(1P33) WILD-TYPE 238   2  14  18
D27V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        78                         238
  R1                         1                           2
  R2                        10                          14
  RX                         7                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P33) MUTATED                                  1     4
  DEL PEAK  2(1P33) WILD-TYPE                                0     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED                          16    57
  DEL PEAK  2(1P33) WILD-TYPE                        38   154
D27V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               16
  WHITE                                                   57
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 38
  WHITE                                                    154
[1] 4 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  3(1P13.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.1) MUTATED    83  28
  DEL PEAK  3(1P13.1) WILD-TYPE 254  65
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          111                           319 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                           28                            65 
$`DEL PEAK  3(1P13.1) 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-3522 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 
       37.05        21.01        13.94        19.99        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 
       19.00        10.06        38.99        37.02        10.06        32.05 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 
       31.07        17.03        24.03         2.01        12.99         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q 
        2.01        21.99        13.05         7.96        38.04        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X 
       15.02        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6901 
        2.96         2.01        41.00        40.96         0.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4615 
        0.20        16.44         0.92        14.50        17.85        32.94 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.13        65.00        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 
        2.24         3.06         2.14         0.26         2.01         8.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       13.02        22.03        14.04        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 
       11.08        10.06        13.51        17.75         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA 
       14.30        13.41        11.38        92.75        49.91       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 
        6.12        14.04        26.47        13.38         1.55        16.24 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 
       35.41         8.35        82.39        23.51        65.85        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.04        91.79        46.75        18.18        10.98 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV 
        9.93        12.00        42.77 

$`DEL PEAK  3(1P13.1) 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-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-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04        19.04        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-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-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       36.03         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02        19.07        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        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-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       27.42        10.88         0.46        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       15.75         0.20        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-4614 
       18.84        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
      100.01        11.74         1.94         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        49.08        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        29.06        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-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-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        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-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 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-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87        16.31        29.59        33.67        13.25         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-G4-6314 
       44.68        55.04        51.75        45.11        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-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 
       70.03 

  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                        17.75                         21.14 
[1] "0.2 - 131.5 (17.8)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.4"
D28V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  3(1P13.1) MUTATED        12        0        5        31         0
  DEL PEAK  3(1P13.1) WILD-TYPE      62        1       23       100         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.1) MUTATED           0         5          3         16
  DEL PEAK  3(1P13.1) WILD-TYPE         1        16          9         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.1) MUTATED           13       23         3         0
  DEL PEAK  3(1P13.1) WILD-TYPE         26       20        15         2
D28V3, multiclass
            clus
vv           DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  STAGE I                             12                            62
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           31                           100
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           3                             9
  STAGE IIIB                          16                            40
  STAGE IIIC                          13                            26
  STAGE IV                            23                            20
  STAGE IVA                            3                            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  3(1P13.1) MUTATED     3  15  82  15
  DEL PEAK  3(1P13.1) WILD-TYPE   8  63 219  37
D28V4, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  T1                           3                             8
  T2                          15                            63
  T3                          82                           219
  T4                          15                            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  3(1P13.1) MUTATED    53  31  31
  DEL PEAK  3(1P13.1) WILD-TYPE 204  73  50
D28V5, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  N0                          53                           204
  N1                          31                            73
  N2                          31                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    74  26
  DEL PEAK  3(1P13.1) WILD-TYPE 248  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     74   26
  DEL PEAK  3(1P13.1) WILD-TYPE  248   36
   clus
vv  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  0                          74                           248
  1                          26                            36
[1] 2 2
[1] FALSE
D28V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    49  66
  DEL PEAK  3(1P13.1) WILD-TYPE 161 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     49   66
  DEL PEAK  3(1P13.1) WILD-TYPE  161  167
        clus
vv       DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  FEMALE                          49                           161
  MALE                            66                           167
[1] 2 2
[1] FALSE
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED   105  10
  DEL PEAK  3(1P13.1) WILD-TYPE 276  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED    105   10
  DEL PEAK  3(1P13.1) WILD-TYPE  276   50
                               clus
vv                              DEL PEAK  3(1P13.1) MUTATED
  COLON ADENOCARCINOMA                                  105
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              DEL PEAK  3(1P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    276
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
D28V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED     1 114
  DEL PEAK  3(1P13.1) WILD-TYPE   2 326
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED      1  114
  DEL PEAK  3(1P13.1) WILD-TYPE    2  326
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  NO                            1                             2
  YES                         114                           326
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.1) MUTATED    74   0  10   8
  DEL PEAK  3(1P13.1) WILD-TYPE 242   3  14  17
D28V10, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  R0                          74                           242
  R1                           0                             3
  R2                          10                            14
  RX                           8                            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"
D28V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1P13.1) MUTATED                                  1     4
  DEL PEAK  3(1P13.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.1) MUTATED                          16    54
  DEL PEAK  3(1P13.1) WILD-TYPE                        38   157
D28V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK  3(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      157
[1] 4 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  4(1Q43) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q43) MUTATED    40  10
  DEL PEAK  4(1Q43) WILD-TYPE 297  83
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         50                         380 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         10                          83 
$`DEL PEAK  4(1Q43) MUTATED`
TCGA-A6-5656 TCGA-A6-5664 TCGA-A6-6138 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3562 
       32.91        22.09        22.52         9.07        21.01        19.99 
TCGA-AA-3673 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3867 TCGA-AA-3966 TCGA-AA-3968 
       50.04        38.99        37.02        24.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 
       16.08         7.96        15.02        41.00         0.79        22.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 
        0.20        16.44        16.31         5.13        29.56         5.23 
TCGA-CA-5256 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5349 
        2.14        49.08         2.01         8.02        22.03        30.08 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6531 
       29.03        13.02        15.02        11.08        10.06        17.75 
TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA 
        1.32        10.13         9.04        13.41        11.38         7.50 
TCGA-DM-A285 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 
        6.12         1.55        33.67         8.35        36.72        36.00 
TCGA-G4-6625 TCGA-NH-A50U 
       91.79        10.98 

$`DEL PEAK  4(1Q43) 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-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 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-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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-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-3841 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        14.93         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-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-3972 TCGA-AA-3973 
       24.00         2.01        20.98        34.03        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-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-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-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-6895 TCGA-AD-6899 
        0.07        21.37         4.21        56.55         0.72         5.79 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        10.88         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-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-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-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-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       13.51        11.51        20.19        20.42        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       15.58         7.53        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 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-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21        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-G4-6320 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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        46.75        47.15        52.80        18.18        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 
       30.28        70.03 

  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                        0.2                         0.0 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                      91.79                      140.38 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                     15.550                      21.255 
[1] "0.2 - 91.8 (15.5)"  "0.0 - 140.4 (21.3)"
[1] "hr=" "1.3"
D29V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  4(1Q43) MUTATED        11        0        2        10         0
  DEL PEAK  4(1Q43) WILD-TYPE      63        1       26       121         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q43) MUTATED           0         2          5          3
  DEL PEAK  4(1Q43) WILD-TYPE         1        19          7         53
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(1Q43) MUTATED            6        8         1         0
  DEL PEAK  4(1Q43) WILD-TYPE         33       35        17         2
D29V3, multiclass
            clus
vv           DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  STAGE I                           11                          63
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                         10                         121
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          2                          19
  STAGE IIIA                         5                           7
  STAGE IIIB                         3                          53
  STAGE IIIC                         6                          33
  STAGE IV                           8                          35
  STAGE IVA                          1                          17
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  4(1Q43) MUTATED     3  13  30   6
  DEL PEAK  4(1Q43) WILD-TYPE   8  65 271  46
D29V4, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  T1                         3                           8
  T2                        13                          65
  T3                        30                         271
  T4                         6                          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  4(1Q43) MUTATED    27  13  12
  DEL PEAK  4(1Q43) WILD-TYPE 230  91  69
D29V5, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  N0                        27                         230
  N1                        13                          91
  N2                        12                          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"
D29V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    33   9
  DEL PEAK  4(1Q43) WILD-TYPE 289  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     33    9
  DEL PEAK  4(1Q43) WILD-TYPE  289   53
   clus
vv  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  0                        33                         289
  1                         9                          53
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    23  29
  DEL PEAK  4(1Q43) WILD-TYPE 187 204
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     23   29
  DEL PEAK  4(1Q43) WILD-TYPE  187  204
        clus
vv       DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  FEMALE                        23                         187
  MALE                          29                         204
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    46   6
  DEL PEAK  4(1Q43) WILD-TYPE 335  54
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     46    6
  DEL PEAK  4(1Q43) WILD-TYPE  335   54
                               clus
vv                              DEL PEAK  4(1Q43) MUTATED
  COLON ADENOCARCINOMA                                 46
  COLON MUCINOUS ADENOCARCINOMA                         6
                               clus
vv                              DEL PEAK  4(1Q43) WILD-TYPE
  COLON ADENOCARCINOMA                                  335
  COLON MUCINOUS ADENOCARCINOMA                          54
[1] 2 2
[1] FALSE
D29V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED     1  51
  DEL PEAK  4(1Q43) WILD-TYPE   2 389
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED      1   51
  DEL PEAK  4(1Q43) WILD-TYPE    2  389
     clus
vv    DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  NO                          1                           2
  YES                        51                         389
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q43) MUTATED    32   1   3   3
  DEL PEAK  4(1Q43) WILD-TYPE 284   2  21  22
D29V10, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  R0                        32                         284
  R1                         1                           2
  R2                         3                          21
  RX                         3                          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"
D29V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(1Q43) MUTATED                                  1     1
  DEL PEAK  4(1Q43) WILD-TYPE                                0    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1Q43) MUTATED                           5    31
  DEL PEAK  4(1Q43) WILD-TYPE                        49   180
D29V12, multiclass
                                  clus
vv                                 DEL PEAK  4(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   31
                                  clus
vv                                 DEL PEAK  4(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 49
  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(30) Variable = DEL PEAK  5(2P21) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(2P21) MUTATED    14   2
  DEL PEAK  5(2P21) WILD-TYPE 323  91
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         414 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                          2                          91 
$`DEL PEAK  5(2P21) MUTATED`
TCGA-A6-2678 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 
       42.28         1.02         6.97        19.99        37.02        12.99 
TCGA-AA-3952 TCGA-AA-A01K TCGA-AA-A01S TCGA-AZ-4313 TCGA-CM-4746 TCGA-CM-5341 
        2.01        31.00         1.02        50.37        37.02        29.06 
TCGA-D5-6534 TCGA-D5-6932 TCGA-F4-6461 TCGA-NH-A50V 
       43.27        11.38        11.11        19.33 

$`DEL PEAK  5(2P21) 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-A6-3810 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-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
        1.02        37.05        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 
       36.03         8.05        19.07         0.00        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
        2.01        24.00        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-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-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         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-A54L 
        0.95        15.75         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84        75.25        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-4747 
        2.93         2.01       124.27        23.05        20.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        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-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-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 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-D5-7000 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-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-G4-6315 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-A5IV TCGA-NH-A6GA 
       47.15        52.80        18.18        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       15.65        12.79        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 

  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                      50.37                      140.38 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     19.660                      20.515 
[1] "1.0 - 50.4 (19.7)"  "0.0 - 140.4 (20.5)"
[1] "hr=" "1.4"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  5(2P21) MUTATED         2        0        2         3         0
  DEL PEAK  5(2P21) WILD-TYPE      72        1       26       128         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2P21) MUTATED           0         1          2          2
  DEL PEAK  5(2P21) WILD-TYPE         1        20         10         54
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2P21) MUTATED            4        0         0         0
  DEL PEAK  5(2P21) WILD-TYPE         35       43        18         2
D30V3, multiclass
            clus
vv           DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  STAGE I                            2                          72
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                          3                         128
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          1                          20
  STAGE IIIA                         2                          10
  STAGE IIIB                         2                          54
  STAGE IIIC                         4                          35
  STAGE IV                           0                          43
  STAGE IVA                          0                          18
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  5(2P21) MUTATED     1   3  10   2
  DEL PEAK  5(2P21) WILD-TYPE  10  75 291  50
D30V4, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  T1                         1                          10
  T2                         3                          75
  T3                        10                         291
  T4                         2                          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  5(2P21) MUTATED     7   4   5
  DEL PEAK  5(2P21) WILD-TYPE 250 100  76
D30V5, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  N0                         7                         250
  N1                         4                         100
  N2                         5                          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"
D30V6, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED    16   0
  DEL PEAK  5(2P21) WILD-TYPE 306  62
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     16    0
  DEL PEAK  5(2P21) WILD-TYPE  306   62
   clus
vv  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  0                        16                         306
  1                         0                          62
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     9   7
  DEL PEAK  5(2P21) WILD-TYPE 201 226
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      9    7
  DEL PEAK  5(2P21) WILD-TYPE  201  226
        clus
vv       DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  FEMALE                         9                         201
  MALE                           7                         226
[1] 2 2
[1] FALSE
D30V8, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED    15   1
  DEL PEAK  5(2P21) WILD-TYPE 366  59
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     15    1
  DEL PEAK  5(2P21) WILD-TYPE  366   59
                               clus
vv                              DEL PEAK  5(2P21) MUTATED
  COLON ADENOCARCINOMA                                 15
  COLON MUCINOUS ADENOCARCINOMA                         1
                               clus
vv                              DEL PEAK  5(2P21) WILD-TYPE
  COLON ADENOCARCINOMA                                  366
  COLON MUCINOUS ADENOCARCINOMA                          59
[1] 2 2
[1] FALSE
D30V9, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     0  16
  DEL PEAK  5(2P21) WILD-TYPE   3 424
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      0   16
  DEL PEAK  5(2P21) WILD-TYPE    3  424
     clus
vv    DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  NO                          0                           3
  YES                        16                         424
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  5(2P21) MUTATED    15   0   0   0
  DEL PEAK  5(2P21) WILD-TYPE 301   3  24  25
D30V10, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  R0                        15                         301
  R1                         0                           3
  R2                         0                          24
  RX                         0                          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"
D30V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2P21) MUTATED                                  0     0
  DEL PEAK  5(2P21) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2P21) MUTATED                           2     6
  DEL PEAK  5(2P21) WILD-TYPE                        52   205
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  5(2P21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  5(2P21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 52
  WHITE                                                    205
[1] 4 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  6(2Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q22.1) MUTATED    16   7
  DEL PEAK  6(2Q22.1) WILD-TYPE 321  86
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           23                           407 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                            7                            86 
$`DEL PEAK  6(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 
       44.32       131.51       117.07         1.55        46.75 

$`DEL PEAK  6(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 
        8.42        31.30         9.70        30.28        70.03 

  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                         1.55                          0.00 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                        24.00                         20.19 
[1] "1.6 - 131.5 (24.0)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(2Q22.1) MUTATED         0        0        1         8         0
  DEL PEAK  6(2Q22.1) WILD-TYPE      74        1       27       123         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q22.1) MUTATED           0         2          1          4
  DEL PEAK  6(2Q22.1) WILD-TYPE         1        19         11         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(2Q22.1) MUTATED            5        2         1         0
  DEL PEAK  6(2Q22.1) WILD-TYPE         34       41        17         2
D31V3, multiclass
            clus
vv           DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  STAGE I                              0                            74
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                            8                           123
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            2                            19
  STAGE IIIA                           1                            11
  STAGE IIIB                           4                            52
  STAGE IIIC                           5                            34
  STAGE IV                             2                            41
  STAGE IVA                            1                            17
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(2Q22.1) MUTATED     0   1  19   4
  DEL PEAK  6(2Q22.1) WILD-TYPE  11  77 282  48
D31V4, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  T1                           0                            11
  T2                           1                            77
  T3                          19                           282
  T4                           4                            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  6(2Q22.1) MUTATED     9   8   7
  DEL PEAK  6(2Q22.1) WILD-TYPE 248  96  74
D31V5, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  N0                           9                           248
  N1                           8                            96
  N2                           7                            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    19   3
  DEL PEAK  6(2Q22.1) WILD-TYPE 303  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     19    3
  DEL PEAK  6(2Q22.1) WILD-TYPE  303   59
   clus
vv  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  0                          19                           303
  1                           3                            59
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    10  14
  DEL PEAK  6(2Q22.1) WILD-TYPE 200 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     10   14
  DEL PEAK  6(2Q22.1) WILD-TYPE  200  219
        clus
vv       DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  FEMALE                          10                           200
  MALE                            14                           219
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    21   3
  DEL PEAK  6(2Q22.1) WILD-TYPE 360  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     21    3
  DEL PEAK  6(2Q22.1) WILD-TYPE  360   57
                               clus
vv                              DEL PEAK  6(2Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   21
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              DEL PEAK  6(2Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    360
  COLON MUCINOUS ADENOCARCINOMA                            57
[1] 2 2
[1] FALSE
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED     0  24
  DEL PEAK  6(2Q22.1) WILD-TYPE   3 416
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED      0   24
  DEL PEAK  6(2Q22.1) WILD-TYPE    3  416
     clus
vv    DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  NO                            0                             3
  YES                          24                           416
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q22.1) MUTATED    16   0   2   1
  DEL PEAK  6(2Q22.1) WILD-TYPE 300   3  22  24
D31V10, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  R0                          16                           300
  R1                           0                             3
  R2                           2                            22
  RX                           1                            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"
D31V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q22.1) MUTATED                                  1     2
  DEL PEAK  6(2Q22.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q22.1) MUTATED                           1     9
  DEL PEAK  6(2Q22.1) WILD-TYPE                        53   202
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK  6(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   53
  WHITE                                                      202
[1] 4 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  7(3P26.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.2) MUTATED    53  15
  DEL PEAK  7(3P26.2) WILD-TYPE 284  78
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           68                           362 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           15                            78 
$`DEL PEAK  7(3P26.2) 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-3529 TCGA-AA-3532 TCGA-AA-3561 
        6.97        38.99         9.07         0.00        29.00        13.94 
TCGA-AA-3662 TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 
        6.05        15.02        85.05        10.06        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       17.03        29.98         2.01        12.99         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F 
       50.99        24.00         7.96        13.94        27.02        32.02 
TCGA-AA-A01K TCGA-AA-A02H TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 
       31.00         2.01        16.44         0.20         5.65         5.13 
TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 
       12.10         3.19         3.29         0.26         2.01         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 
       13.02        29.06        22.03         5.03        14.04        11.08 
TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.01        20.19        17.75         1.32        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA 
       17.85        13.41        11.38         7.50        13.38         9.93 
TCGA-QG-A5YV TCGA-RU-A8FL 
       42.77        30.28 

$`DEL PEAK  7(3P26.2) 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-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       19.99        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04        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-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       14.93         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 
        0.00        36.03         0.99        31.07        53.00        24.03 
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-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       24.00         2.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       34.06        26.01        25.02        27.02        19.07        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       38.04         4.01        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-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         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-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        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-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-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-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-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-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       20.42        18.25         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67        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-A6GB TCGA-NH-A6GC 
       18.18        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-QL-A97D TCGA-WS-AB45 
        9.70        70.03 

  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                            0                             0 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                       14.285                        21.990 
[1] "0.0 - 85.0 (14.3)"  "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P26.2) MUTATED         6        0        1        19         0
  DEL PEAK  7(3P26.2) WILD-TYPE      68        1       27       112         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.2) MUTATED           0         4          2         11
  DEL PEAK  7(3P26.2) WILD-TYPE         1        17         10         45
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.2) MUTATED            8       14         4         0
  DEL PEAK  7(3P26.2) WILD-TYPE         31       29        14         2
D32V3, multiclass
            clus
vv           DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  STAGE I                              6                            68
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           19                           112
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           2                            10
  STAGE IIIB                          11                            45
  STAGE IIIC                           8                            31
  STAGE IV                            14                            29
  STAGE IVA                            4                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(3P26.2) MUTATED     2   6  51  10
  DEL PEAK  7(3P26.2) WILD-TYPE   9  72 250  42
D32V4, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  T1                           2                             9
  T2                           6                            72
  T3                          51                           250
  T4                          10                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  7(3P26.2) MUTATED    29  21  19
  DEL PEAK  7(3P26.2) WILD-TYPE 228  83  62
D32V5, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  N0                          29                           228
  N1                          21                            83
  N2                          19                            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"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    42  18
  DEL PEAK  7(3P26.2) WILD-TYPE 280  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     42   18
  DEL PEAK  7(3P26.2) WILD-TYPE  280   44
   clus
vv  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  0                          42                           280
  1                          18                            44
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    32  37
  DEL PEAK  7(3P26.2) WILD-TYPE 178 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     32   37
  DEL PEAK  7(3P26.2) WILD-TYPE  178  196
        clus
vv       DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  FEMALE                          32                           178
  MALE                            37                           196
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    65   4
  DEL PEAK  7(3P26.2) WILD-TYPE 316  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     65    4
  DEL PEAK  7(3P26.2) WILD-TYPE  316   56
                               clus
vv                              DEL PEAK  7(3P26.2) MUTATED
  COLON ADENOCARCINOMA                                   65
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK  7(3P26.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    316
  COLON MUCINOUS ADENOCARCINOMA                            56
[1] 2 2
[1] FALSE
D32V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED     0  69
  DEL PEAK  7(3P26.2) WILD-TYPE   3 371
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED      0   69
  DEL PEAK  7(3P26.2) WILD-TYPE    3  371
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  NO                            0                             3
  YES                          69                           371
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.2) MUTATED    49   0   7   4
  DEL PEAK  7(3P26.2) WILD-TYPE 267   3  17  21
D32V10, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  R0                          49                           267
  R1                           0                             3
  R2                           7                            17
  RX                           4                            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"
D32V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P26.2) MUTATED                                  0     2
  DEL PEAK  7(3P26.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P26.2) MUTATED                           7    32
  DEL PEAK  7(3P26.2) WILD-TYPE                        47   179
D32V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     32
                                  clus
vv                                 DEL PEAK  7(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      179
[1] 4 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  8(3P14.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.2) MUTATED    65  17
  DEL PEAK  8(3P14.2) WILD-TYPE 272  76
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           82                           348 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           17                            76 
$`DEL PEAK  8(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 
       12.00        42.77        30.28        70.03 

$`DEL PEAK  8(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 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                       119.70                        140.38 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                       16.375                        21.990 
[1] "0.2 - 119.7 (16.4)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3P14.2) MUTATED        10        0        2        24         0
  DEL PEAK  8(3P14.2) WILD-TYPE      64        1       26       107         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED           0         5          1         14
  DEL PEAK  8(3P14.2) WILD-TYPE         1        16         11         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3P14.2) MUTATED           11       11         5         1
  DEL PEAK  8(3P14.2) WILD-TYPE         28       32        13         1
D33V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                             10                            64
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           24                           107
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           1                            11
  STAGE IIIB                          14                            42
  STAGE IIIC                          11                            28
  STAGE IV                            11                            32
  STAGE IVA                            5                            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  8(3P14.2) MUTATED     3   9  59  14
  DEL PEAK  8(3P14.2) WILD-TYPE   8  69 242  38
D33V4, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T1                           3                             8
  T2                           9                            69
  T3                          59                           242
  T4                          14                            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  8(3P14.2) MUTATED    40  23  22
  DEL PEAK  8(3P14.2) WILD-TYPE 217  81  59
D33V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          40                           217
  N1                          23                            81
  N2                          22                            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    55  17
  DEL PEAK  8(3P14.2) WILD-TYPE 267  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     55   17
  DEL PEAK  8(3P14.2) WILD-TYPE  267   45
   clus
vv  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  0                          55                           267
  1                          17                            45
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    43  42
  DEL PEAK  8(3P14.2) WILD-TYPE 167 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     43   42
  DEL PEAK  8(3P14.2) WILD-TYPE  167  191
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          43                           167
  MALE                            42                           191
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    76   9
  DEL PEAK  8(3P14.2) WILD-TYPE 305  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     76    9
  DEL PEAK  8(3P14.2) WILD-TYPE  305   51
                               clus
vv                              DEL PEAK  8(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                   76
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK  8(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    305
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED     0  85
  DEL PEAK  8(3P14.2) WILD-TYPE   3 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      0   85
  DEL PEAK  8(3P14.2) WILD-TYPE    3  355
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                            0                             3
  YES                          85                           355
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P14.2) MUTATED    60   1   6   4
  DEL PEAK  8(3P14.2) WILD-TYPE 256   2  18  21
D33V10, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                          60                           256
  R1                           1                             2
  R2                           6                            18
  RX                           4                            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"
D33V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P14.2) MUTATED                                  0     2
  DEL PEAK  8(3P14.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED                          12    39
  DEL PEAK  8(3P14.2) WILD-TYPE                        42   172
D33V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     39
                                  clus
vv                                 DEL PEAK  8(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      172
[1] 4 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  9(3Q26.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(3Q26.31) MUTATED    34  10
  DEL PEAK  9(3Q26.31) WILD-TYPE 303  83
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            386 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            10                             83 
$`DEL PEAK  9(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 
       42.77        30.28 

$`DEL PEAK  9(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 
        9.70        70.03 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             0                              0 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        15.385                         21.075 
[1] "0.0 - 131.5 (15.4)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.2"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(3Q26.31) MUTATED         4        0        0        15         0
  DEL PEAK  9(3Q26.31) WILD-TYPE      70        1       28       116         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q26.31) MUTATED           0         3          0          5
  DEL PEAK  9(3Q26.31) WILD-TYPE         1        18         12         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(3Q26.31) MUTATED            8        6         3         0
  DEL PEAK  9(3Q26.31) WILD-TYPE         31       37        15         2
D34V3, multiclass
            clus
vv           DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  STAGE I                               4                             70
  STAGE IA                              0                              1
  STAGE II                              0                             28
  STAGE IIA                            15                            116
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            0                             12
  STAGE IIIB                            5                             51
  STAGE IIIC                            8                             31
  STAGE IV                              6                             37
  STAGE IVA                             3                             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(3Q26.31) MUTATED     0   4  32   8
  DEL PEAK  9(3Q26.31) WILD-TYPE  11  74 269  44
D34V4, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T1                            0                             11
  T2                            4                             74
  T3                           32                            269
  T4                            8                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  9(3Q26.31) MUTATED    22  10  12
  DEL PEAK  9(3Q26.31) WILD-TYPE 235  94  69
D34V5, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                           22                            235
  N1                           10                             94
  N2                           12                             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"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    30   9
  DEL PEAK  9(3Q26.31) WILD-TYPE 292  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     30    9
  DEL PEAK  9(3Q26.31) WILD-TYPE  292   53
   clus
vv  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  0                           30                            292
  1                            9                             53
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    22  22
  DEL PEAK  9(3Q26.31) WILD-TYPE 188 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     22   22
  DEL PEAK  9(3Q26.31) WILD-TYPE  188  211
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                           22                            188
  MALE                             22                            211
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    41   3
  DEL PEAK  9(3Q26.31) WILD-TYPE 340  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     41    3
  DEL PEAK  9(3Q26.31) WILD-TYPE  340   57
                               clus
vv                              DEL PEAK  9(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                    41
  COLON MUCINOUS ADENOCARCINOMA                            3
                               clus
vv                              DEL PEAK  9(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                     340
  COLON MUCINOUS ADENOCARCINOMA                             57
[1] 2 2
[1] FALSE
D34V9, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED     0  44
  DEL PEAK  9(3Q26.31) WILD-TYPE   3 396
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      0   44
  DEL PEAK  9(3Q26.31) WILD-TYPE    3  396
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  NO                             0                              3
  YES                           44                            396
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(3Q26.31) MUTATED    34   0   2   1
  DEL PEAK  9(3Q26.31) WILD-TYPE 282   3  22  24
D34V10, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  R0                           34                            282
  R1                            0                              3
  R2                            2                             22
  RX                            1                             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"
D34V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(3Q26.31) MUTATED                                  0     1
  DEL PEAK  9(3Q26.31) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q26.31) MUTATED                           7    22
  DEL PEAK  9(3Q26.31) WILD-TYPE                        47   189
D34V12, multiclass
                                  clus
vv                                 DEL PEAK  9(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK  9(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       189
[1] 4 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 10(4P16.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4P16.2) MUTATED    93  35
  DEL PEAK 10(4P16.2) WILD-TYPE 244  58
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          128                           302 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                           35                            58 
$`DEL PEAK 10(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 
       29.46         9.70 

$`DEL PEAK 10(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 
       30.28        70.03 

  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                        91.79                        140.38 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                       20.235                        20.515 
[1] "0.2 - 91.8 (20.2)"  "0.0 - 140.4 (20.5)"
[1] "hr=" "1.7"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4P16.2) MUTATED        16        0        6        30         2
  DEL PEAK 10(4P16.2) WILD-TYPE      58        1       22       101         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4P16.2) MUTATED           0         5          6         15
  DEL PEAK 10(4P16.2) WILD-TYPE         1        16          6         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4P16.2) MUTATED           16       26         7         0
  DEL PEAK 10(4P16.2) WILD-TYPE         23       17        11         2
D35V3, multiclass
            clus
vv           DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  STAGE I                             16                            58
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           30                           101
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           6                             6
  STAGE IIIB                          15                            41
  STAGE IIIC                          16                            23
  STAGE IV                            26                            17
  STAGE IVA                            7                            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 10(4P16.2) MUTATED     4  20  89  20
  DEL PEAK 10(4P16.2) WILD-TYPE   7  58 212  32
D35V4, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  T1                           4                             7
  T2                          20                            58
  T3                          89                           212
  T4                          20                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 10(4P16.2) MUTATED    58  39  36
  DEL PEAK 10(4P16.2) WILD-TYPE 199  65  45
D35V5, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  N0                          58                           199
  N1                          39                            65
  N2                          36                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED    80  33
  DEL PEAK 10(4P16.2) WILD-TYPE 242  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED     80   33
  DEL PEAK 10(4P16.2) WILD-TYPE  242   29
   clus
vv  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  0                          80                           242
  1                          33                            29
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED    60  73
  DEL PEAK 10(4P16.2) WILD-TYPE 150 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED     60   73
  DEL PEAK 10(4P16.2) WILD-TYPE  150  160
        clus
vv       DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  FEMALE                          60                           150
  MALE                            73                           160
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED   121  11
  DEL PEAK 10(4P16.2) WILD-TYPE 260  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED    121   11
  DEL PEAK 10(4P16.2) WILD-TYPE  260   49
                               clus
vv                              DEL PEAK 10(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                  121
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              DEL PEAK 10(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    260
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED     3 130
  DEL PEAK 10(4P16.2) WILD-TYPE   0 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED      3  130
  DEL PEAK 10(4P16.2) WILD-TYPE    0  310
     clus
vv    DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  NO                            3                             0
  YES                         130                           310
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4P16.2) MUTATED    93   0  13   5
  DEL PEAK 10(4P16.2) WILD-TYPE 223   3  11  20
D35V10, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  R0                          93                           223
  R1                           0                             3
  R2                          13                            11
  RX                           5                            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"
D35V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4P16.2) MUTATED                                  1     2
  DEL PEAK 10(4P16.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4P16.2) MUTATED                          16    61
  DEL PEAK 10(4P16.2) WILD-TYPE                        38   150
D35V12, multiclass
                                  clus
vv                                 DEL PEAK 10(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     61
                                  clus
vv                                 DEL PEAK 10(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      150
[1] 4 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 11(4Q22.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q22.1) MUTATED   104  38
  DEL PEAK 11(4Q22.1) WILD-TYPE 233  55
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          142                           288 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                           38                            55 
$`DEL PEAK 11(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 
       42.77        29.46         9.70        30.28 

$`DEL PEAK 11(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 

  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                            0                             0 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                       102.44                        140.38 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                       20.235                        20.515 
[1] "0.0 - 102.4 (20.2)" "0.0 - 140.4 (20.5)"
[1] "hr=" "1.6"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q22.1) MUTATED        14        0        8        37         2
  DEL PEAK 11(4Q22.1) WILD-TYPE      60        1       20        94         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q22.1) MUTATED           0         3          7         23
  DEL PEAK 11(4Q22.1) WILD-TYPE         1        18          5         33
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q22.1) MUTATED           19       21         6         1
  DEL PEAK 11(4Q22.1) WILD-TYPE         20       22        12         1
D36V3, multiclass
            clus
vv           DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  STAGE I                             14                            60
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           37                            94
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           7                             5
  STAGE IIIB                          23                            33
  STAGE IIIC                          19                            20
  STAGE IV                            21                            22
  STAGE IVA                            6                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(4Q22.1) MUTATED     4  18 102  21
  DEL PEAK 11(4Q22.1) WILD-TYPE   7  60 199  31
D36V4, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  T1                           4                             7
  T2                          18                            60
  T3                         102                           199
  T4                          21                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 11(4Q22.1) MUTATED    64  44  37
  DEL PEAK 11(4Q22.1) WILD-TYPE 193  60  44
D36V5, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  N0                          64                           193
  N1                          44                            60
  N2                          37                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    94  28
  DEL PEAK 11(4Q22.1) WILD-TYPE 228  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     94   28
  DEL PEAK 11(4Q22.1) WILD-TYPE  228   34
   clus
vv  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  0                          94                           228
  1                          28                            34
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    64  81
  DEL PEAK 11(4Q22.1) WILD-TYPE 146 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     64   81
  DEL PEAK 11(4Q22.1) WILD-TYPE  146  152
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  FEMALE                          64                           146
  MALE                            81                           152
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED   133  11
  DEL PEAK 11(4Q22.1) WILD-TYPE 248  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED    133   11
  DEL PEAK 11(4Q22.1) WILD-TYPE  248   49
                               clus
vv                              DEL PEAK 11(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                  133
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              DEL PEAK 11(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    248
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED     3 142
  DEL PEAK 11(4Q22.1) WILD-TYPE   0 298
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED      3  142
  DEL PEAK 11(4Q22.1) WILD-TYPE    0  298
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  NO                            3                             0
  YES                         142                           298
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q22.1) MUTATED   104   1   9   7
  DEL PEAK 11(4Q22.1) WILD-TYPE 212   2  15  18
D36V10, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  R0                         104                           212
  R1                           1                             2
  R2                           9                            15
  RX                           7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q22.1) MUTATED                                  0     3
  DEL PEAK 11(4Q22.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q22.1) MUTATED                          22    70
  DEL PEAK 11(4Q22.1) WILD-TYPE                        32   141
D36V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                     70
                                  clus
vv                                 DEL PEAK 11(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      141
[1] 4 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 12(4Q35.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q35.1) MUTATED   115  34
  DEL PEAK 12(4Q35.1) WILD-TYPE 222  59
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          149                           281 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                           34                            59 
$`DEL PEAK 12(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-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       29.16        24.13        25.08        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-A69D TCGA-AZ-4308 
        0.20        14.50        16.31         0.95        17.85        75.25 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 
        5.65         5.13        65.00        12.10        29.56         2.24 
TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 
        2.14         0.10         1.35        49.08         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        22.03        30.08         5.03        15.02        15.02 
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-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.08        11.01        45.40        13.51        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 
        1.32        43.27        17.85         7.53         9.04        13.41 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       13.32       140.38         7.50        44.32       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
       14.04        26.47        13.38         1.55        16.24        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 
       35.41         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-A6GC 
       91.79        46.75        18.18        10.98         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       12.00        42.77        29.46         9.70        30.28 

$`DEL PEAK 12(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-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 
       32.71        27.09        22.52         8.38        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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       15.75         0.20        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       18.84        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         3.19         1.94         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         0.33        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       25.02        26.04        27.02        22.98        16.01        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-6676 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       12.26        19.59        11.51        20.42        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        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-D5-6931 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-A1HB TCGA-DM-A280 
      130.65        92.75        49.91        12.59       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
        6.18        35.87        16.31        29.59        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       19.43       107.67        28.21        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-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       13.05        32.98         8.42        31.30        70.03 

  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          0.1                           0.0 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                        21.76                         19.66 
[1] "0.1 - 140.4 (21.8)" "0.0 - 139.2 (19.7)"
[1] "hr=" "1.1"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(4Q35.1) MUTATED        17        0        7        42         1
  DEL PEAK 12(4Q35.1) WILD-TYPE      57        1       21        89         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q35.1) MUTATED           0         7          6         21
  DEL PEAK 12(4Q35.1) WILD-TYPE         1        14          6         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(4Q35.1) MUTATED           18       23         7         1
  DEL PEAK 12(4Q35.1) WILD-TYPE         21       20        11         1
D37V3, multiclass
            clus
vv           DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  STAGE I                             17                            57
  STAGE IA                             0                             1
  STAGE II                             7                            21
  STAGE IIA                           42                            89
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            7                            14
  STAGE IIIA                           6                             6
  STAGE IIIB                          21                            35
  STAGE IIIC                          18                            21
  STAGE IV                            23                            20
  STAGE IVA                            7                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(4Q35.1) MUTATED     4  21 106  22
  DEL PEAK 12(4Q35.1) WILD-TYPE   7  57 195  30
D37V4, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  T1                           4                             7
  T2                          21                            57
  T3                         106                           195
  T4                          22                            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 12(4Q35.1) MUTATED    71  44  38
  DEL PEAK 12(4Q35.1) WILD-TYPE 186  60  43
D37V5, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  N0                          71                           186
  N1                          44                            60
  N2                          38                            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"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   103  31
  DEL PEAK 12(4Q35.1) WILD-TYPE 219  31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    103   31
  DEL PEAK 12(4Q35.1) WILD-TYPE  219   31
   clus
vv  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  0                         103                           219
  1                          31                            31
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED    78  75
  DEL PEAK 12(4Q35.1) WILD-TYPE 132 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED     78   75
  DEL PEAK 12(4Q35.1) WILD-TYPE  132  158
        clus
vv       DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  FEMALE                          78                           132
  MALE                            75                           158
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   137  15
  DEL PEAK 12(4Q35.1) WILD-TYPE 244  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    137   15
  DEL PEAK 12(4Q35.1) WILD-TYPE  244   45
                               clus
vv                              DEL PEAK 12(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                  137
  COLON MUCINOUS ADENOCARCINOMA                          15
                               clus
vv                              DEL PEAK 12(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    244
  COLON MUCINOUS ADENOCARCINOMA                            45
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED     3 150
  DEL PEAK 12(4Q35.1) WILD-TYPE   0 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED      3  150
  DEL PEAK 12(4Q35.1) WILD-TYPE    0  290
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  NO                            3                             0
  YES                         150                           290
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q35.1) MUTATED   106   1  12   8
  DEL PEAK 12(4Q35.1) WILD-TYPE 210   2  12  17
D37V10, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  R0                         106                           210
  R1                           1                             2
  R2                          12                            12
  RX                           8                            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"
D37V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(4Q35.1) MUTATED                                  1     4
  DEL PEAK 12(4Q35.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q35.1) MUTATED                          23    68
  DEL PEAK 12(4Q35.1) WILD-TYPE                        31   143
D37V12, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 23
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK 12(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      143
[1] 4 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 13(5Q12.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q12.1) MUTATED    74  27
  DEL PEAK 13(5Q12.1) WILD-TYPE 263  66
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          101                           329 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                           27                            66 
$`DEL PEAK 13(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 
       12.79        42.77         8.42         9.70        30.28 

$`DEL PEAK 13(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 
       12.00        29.46        32.98        31.30        70.03 

  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                        22.42                         20.02 
[1] "0.2 - 131.5 (22.4)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.4"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q12.1) MUTATED        17        0        4        18         1
  DEL PEAK 13(5Q12.1) WILD-TYPE      57        1       24       113         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q12.1) MUTATED           0         4          6         13
  DEL PEAK 13(5Q12.1) WILD-TYPE         1        17          6         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q12.1) MUTATED           15       12         8         1
  DEL PEAK 13(5Q12.1) WILD-TYPE         24       31        10         1
D38V3, multiclass
            clus
vv           DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  STAGE I                             17                            57
  STAGE IA                             0                             1
  STAGE II                             4                            24
  STAGE IIA                           18                           113
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             6
  STAGE IIIB                          13                            43
  STAGE IIIC                          15                            24
  STAGE IV                            12                            31
  STAGE IVA                            8                            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 13(5Q12.1) MUTATED     3  20  67  13
  DEL PEAK 13(5Q12.1) WILD-TYPE   8  58 234  39
D38V4, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  T1                           3                             8
  T2                          20                            58
  T3                          67                           234
  T4                          13                            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 13(5Q12.1) MUTATED    47  29  27
  DEL PEAK 13(5Q12.1) WILD-TYPE 210  75  54
D38V5, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  N0                          47                           210
  N1                          29                            75
  N2                          27                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED    65  21
  DEL PEAK 13(5Q12.1) WILD-TYPE 257  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED     65   21
  DEL PEAK 13(5Q12.1) WILD-TYPE  257   41
   clus
vv  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  0                          65                           257
  1                          21                            41
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED    44  59
  DEL PEAK 13(5Q12.1) WILD-TYPE 166 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED     44   59
  DEL PEAK 13(5Q12.1) WILD-TYPE  166  174
        clus
vv       DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  FEMALE                          44                           166
  MALE                            59                           174
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED    95   8
  DEL PEAK 13(5Q12.1) WILD-TYPE 286  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED     95    8
  DEL PEAK 13(5Q12.1) WILD-TYPE  286   52
                               clus
vv                              DEL PEAK 13(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   95
  COLON MUCINOUS ADENOCARCINOMA                           8
                               clus
vv                              DEL PEAK 13(5Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    286
  COLON MUCINOUS ADENOCARCINOMA                            52
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED     3 100
  DEL PEAK 13(5Q12.1) WILD-TYPE   0 340
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED      3  100
  DEL PEAK 13(5Q12.1) WILD-TYPE    0  340
     clus
vv    DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  NO                            3                             0
  YES                         100                           340
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q12.1) MUTATED    69   1   6   4
  DEL PEAK 13(5Q12.1) WILD-TYPE 247   2  18  21
D38V10, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  R0                          69                           247
  R1                           1                             2
  R2                           6                            18
  RX                           4                            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"
D38V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q12.1) MUTATED                                  1     2
  DEL PEAK 13(5Q12.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q12.1) MUTATED                          15    53
  DEL PEAK 13(5Q12.1) WILD-TYPE                        39   158
D38V12, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK 13(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      158
[1] 4 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 14(5Q21.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q21.1) MUTATED    90  32
  DEL PEAK 14(5Q21.1) WILD-TYPE 247  61
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          122                           308 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                           32                            61 
$`DEL PEAK 14(5Q21.1) 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-3496 TCGA-AA-3518 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-3556 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 
       13.02        24.00        23.01        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-A01C TCGA-AA-A01D 
       27.02        34.03        27.02        42.02        15.02        10.98 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 
       33.04         2.96         2.01         5.03        41.00        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A71X TCGA-AZ-4614 
       27.42         0.20        16.31         0.20        19.33         5.65 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
       83.80        65.00        62.79        29.56         5.23         1.94 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
        3.29         1.35        49.08        25.02        26.04         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       13.02        29.06        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 
       29.03        13.02        13.05        19.59        20.42        15.12 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       17.85        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 
       92.75       140.38        44.32         7.76         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       26.47       117.07        98.24         8.61        13.38         1.55 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 
       33.67         8.35        82.39        45.11        36.00        91.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5Z1 
       18.18        10.98        12.79        42.77        29.46         8.42 
TCGA-QL-A97D TCGA-RU-A8FL 
        9.70        30.28 

$`DEL PEAK 14(5Q21.1) 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-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02         1.02        37.05        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 
       29.95        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-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-A01F TCGA-AA-A01G 
       14.99        21.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         5.79 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       10.88        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        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-6599 TCGA-AZ-6600 
        5.13        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
      100.01        11.74         3.19         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.25         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       37.02        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 
       12.26        13.51        11.51        20.19        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58         7.53        12.39        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        49.91        13.32        12.59         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      135.65       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24        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-G4-6311 
       65.85        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        46.75        47.15        52.80        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
       19.33         9.93        15.65        13.05        12.00        32.98 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       31.30        70.03 

  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                       21.090                        20.235 
[1] "0.2 - 140.4 (21.1)" "0.0 - 139.2 (20.2)"
[1] "hr=" "1.3"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q21.1) MUTATED        18        0        5        25         0
  DEL PEAK 14(5Q21.1) WILD-TYPE      56        1       23       106         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q21.1) MUTATED           0         4          8         17
  DEL PEAK 14(5Q21.1) WILD-TYPE         1        17          4         39
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q21.1) MUTATED           17       16         8         2
  DEL PEAK 14(5Q21.1) WILD-TYPE         22       27        10         0
D39V3, multiclass
            clus
vv           DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  STAGE I                             18                            56
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           25                           106
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           8                             4
  STAGE IIIB                          17                            39
  STAGE IIIC                          17                            22
  STAGE IV                            16                            27
  STAGE IVA                            8                            10
  STAGE IVB                            2                             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(5Q21.1) MUTATED     3  22  84  15
  DEL PEAK 14(5Q21.1) WILD-TYPE   8  56 217  37
D39V4, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  T1                           3                             8
  T2                          22                            56
  T3                          84                           217
  T4                          15                            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 14(5Q21.1) MUTATED    55  37  32
  DEL PEAK 14(5Q21.1) WILD-TYPE 202  67  49
D39V5, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  N0                          55                           202
  N1                          37                            67
  N2                          32                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED    80  26
  DEL PEAK 14(5Q21.1) WILD-TYPE 242  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED     80   26
  DEL PEAK 14(5Q21.1) WILD-TYPE  242   36
   clus
vv  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  0                          80                           242
  1                          26                            36
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED    54  70
  DEL PEAK 14(5Q21.1) WILD-TYPE 156 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED     54   70
  DEL PEAK 14(5Q21.1) WILD-TYPE  156  163
        clus
vv       DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  FEMALE                          54                           156
  MALE                            70                           163
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED   109  14
  DEL PEAK 14(5Q21.1) WILD-TYPE 272  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED    109   14
  DEL PEAK 14(5Q21.1) WILD-TYPE  272   46
                               clus
vv                              DEL PEAK 14(5Q21.1) MUTATED
  COLON ADENOCARCINOMA                                  109
  COLON MUCINOUS ADENOCARCINOMA                          14
                               clus
vv                              DEL PEAK 14(5Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    272
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED     3 121
  DEL PEAK 14(5Q21.1) WILD-TYPE   0 319
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED      3  121
  DEL PEAK 14(5Q21.1) WILD-TYPE    0  319
     clus
vv    DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  NO                            3                             0
  YES                         121                           319
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q21.1) MUTATED    80   1   9   5
  DEL PEAK 14(5Q21.1) WILD-TYPE 236   2  15  20
D39V10, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  R0                          80                           236
  R1                           1                             2
  R2                           9                            15
  RX                           5                            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"
D39V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q21.1) MUTATED                                  1     2
  DEL PEAK 14(5Q21.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q21.1) MUTATED                          15    63
  DEL PEAK 14(5Q21.1) WILD-TYPE                        39   148
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 14(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      148
[1] 4 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 15(5Q22.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q22.2) MUTATED    89  33
  DEL PEAK 15(5Q22.2) WILD-TYPE 248  60
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          122                           308 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                           33                            60 
$`DEL PEAK 15(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 
        9.70        30.28 

$`DEL PEAK 15(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 
       31.30        70.03 

  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                       19.460                        20.795 
[1] "0.2 - 140.4 (19.5)" "0.0 - 139.2 (20.8)"
[1] "hr=" "1.4"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(5Q22.2) MUTATED        19        0        6        28         0
  DEL PEAK 15(5Q22.2) WILD-TYPE      55        1       22       103         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q22.2) MUTATED           0         5          7         15
  DEL PEAK 15(5Q22.2) WILD-TYPE         1        16          5         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(5Q22.2) MUTATED           15       18         8         1
  DEL PEAK 15(5Q22.2) WILD-TYPE         24       25        10         1
D40V3, multiclass
            clus
vv           DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  STAGE I                             19                            55
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           28                           103
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           7                             5
  STAGE IIIB                          15                            41
  STAGE IIIC                          15                            24
  STAGE IV                            18                            25
  STAGE IVA                            8                            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 15(5Q22.2) MUTATED     3  22  87  15
  DEL PEAK 15(5Q22.2) WILD-TYPE   8  56 214  37
D40V4, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  T1                           3                             8
  T2                          22                            56
  T3                          87                           214
  T4                          15                            37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 15(5Q22.2) MUTATED    62  34  31
  DEL PEAK 15(5Q22.2) WILD-TYPE 195  70  50
D40V5, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  N0                          62                           195
  N1                          34                            70
  N2                          31                            50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED    79  27
  DEL PEAK 15(5Q22.2) WILD-TYPE 243  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED     79   27
  DEL PEAK 15(5Q22.2) WILD-TYPE  243   35
   clus
vv  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  0                          79                           243
  1                          27                            35
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED    53  74
  DEL PEAK 15(5Q22.2) WILD-TYPE 157 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED     53   74
  DEL PEAK 15(5Q22.2) WILD-TYPE  157  159
        clus
vv       DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  FEMALE                          53                           157
  MALE                            74                           159
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED   115  12
  DEL PEAK 15(5Q22.2) WILD-TYPE 266  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED    115   12
  DEL PEAK 15(5Q22.2) WILD-TYPE  266   48
                               clus
vv                              DEL PEAK 15(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                  115
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              DEL PEAK 15(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    266
  COLON MUCINOUS ADENOCARCINOMA                            48
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED     3 124
  DEL PEAK 15(5Q22.2) WILD-TYPE   0 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED      3  124
  DEL PEAK 15(5Q22.2) WILD-TYPE    0  316
     clus
vv    DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  NO                            3                             0
  YES                         124                           316
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q22.2) MUTATED    78   1  11   6
  DEL PEAK 15(5Q22.2) WILD-TYPE 238   2  13  19
D40V10, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  R0                          78                           238
  R1                           1                             2
  R2                          11                            13
  RX                           6                            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"
D40V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(5Q22.2) MUTATED                                  1     3
  DEL PEAK 15(5Q22.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q22.2) MUTATED                          13    66
  DEL PEAK 15(5Q22.2) WILD-TYPE                        41   145
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 15(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK 15(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   41
  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(41) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    39  14
  DEL PEAK 16(6P25.3) WILD-TYPE 298  79
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           53                           377 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           14                            79 
$`DEL PEAK 16(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 
       13.32        26.47       117.07        33.67        36.00 

$`DEL PEAK 16(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 
        8.42        31.30         9.70        30.28        70.03 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.72                          0.00 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                       117.07                        140.38 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                        19.04                         20.98 
[1] "0.7 - 117.1 (19.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6P25.3) MUTATED         7        0        6        17         1
  DEL PEAK 16(6P25.3) WILD-TYPE      67        1       22       114         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED           0         3          1          3
  DEL PEAK 16(6P25.3) WILD-TYPE         1        18         11         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6P25.3) MUTATED            5        5         4         0
  DEL PEAK 16(6P25.3) WILD-TYPE         34       38        14         2
D41V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              7                            67
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           17                           114
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           1                            11
  STAGE IIIB                           3                            53
  STAGE IIIC                           5                            34
  STAGE IV                             5                            38
  STAGE IVA                            4                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(6P25.3) MUTATED     2   7  36   9
  DEL PEAK 16(6P25.3) WILD-TYPE   9  71 265  43
D41V4, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           2                             9
  T2                           7                            71
  T3                          36                           265
  T4                           9                            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 16(6P25.3) MUTATED    32  11  11
  DEL PEAK 16(6P25.3) WILD-TYPE 225  93  70
D41V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          32                           225
  N1                          11                            93
  N2                          11                            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"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    37   9
  DEL PEAK 16(6P25.3) WILD-TYPE 285  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     37    9
  DEL PEAK 16(6P25.3) WILD-TYPE  285   53
   clus
vv  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  0                          37                           285
  1                           9                            53
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    19  35
  DEL PEAK 16(6P25.3) WILD-TYPE 191 198
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     19   35
  DEL PEAK 16(6P25.3) WILD-TYPE  191  198
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          19                           191
  MALE                            35                           198
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    49   5
  DEL PEAK 16(6P25.3) WILD-TYPE 332  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     49    5
  DEL PEAK 16(6P25.3) WILD-TYPE  332   55
                               clus
vv                              DEL PEAK 16(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                   49
  COLON MUCINOUS ADENOCARCINOMA                           5
                               clus
vv                              DEL PEAK 16(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    332
  COLON MUCINOUS ADENOCARCINOMA                            55
[1] 2 2
[1] FALSE
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     0  54
  DEL PEAK 16(6P25.3) WILD-TYPE   3 386
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      0   54
  DEL PEAK 16(6P25.3) WILD-TYPE    3  386
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                            0                             3
  YES                          54                           386
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    37   0   1   5
  DEL PEAK 16(6P25.3) WILD-TYPE 279   3  23  20
D41V10, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          37                           279
  R1                           0                             3
  R2                           1                            23
  RX                           5                            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"
D41V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6P25.3) MUTATED                                  0     3
  DEL PEAK 16(6P25.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6P25.3) MUTATED                           1    26
  DEL PEAK 16(6P25.3) WILD-TYPE                        53   185
D41V12, multiclass
                                  clus
vv                                 DEL PEAK 16(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     26
                                  clus
vv                                 DEL PEAK 16(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   53
  WHITE                                                      185
[1] 4 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 17(6Q26) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    40  19
  DEL PEAK 17(6Q26) WILD-TYPE 297  74
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         59                         371 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         19                          74 
$`DEL PEAK 17(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 
      131.51         1.55        33.67        82.39         9.93 

$`DEL PEAK 17(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 
        8.42        31.30         9.70        30.28        70.03 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        0.2                         0.0 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     131.51                      140.38 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      17.75                       21.37 
[1] "0.2 - 131.5 (17.8)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1.8"
D42V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(6Q26) MUTATED         8        0        6        11         1
  DEL PEAK 17(6Q26) WILD-TYPE      66        1       22       120         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           0         4          0          8
  DEL PEAK 17(6Q26) WILD-TYPE         1        17         12         48
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(6Q26) MUTATED            9        9         4         1
  DEL PEAK 17(6Q26) WILD-TYPE         30       34        14         1
D42V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            8                          66
  STAGE IA                           0                           1
  STAGE II                           6                          22
  STAGE IIA                         11                         120
  STAGE IIB                          1                           7
  STAGE IIC                          0                           1
  STAGE III                          4                          17
  STAGE IIIA                         0                          12
  STAGE IIIB                         8                          48
  STAGE IIIC                         9                          30
  STAGE IV                           9                          34
  STAGE IVA                          4                          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 17(6Q26) MUTATED     2   7  43   9
  DEL PEAK 17(6Q26) WILD-TYPE   9  71 258  43
D42V4, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T1                         2                           9
  T2                         7                          71
  T3                        43                         258
  T4                         9                          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 17(6Q26) MUTATED    26  14  21
  DEL PEAK 17(6Q26) WILD-TYPE 231  90  60
D42V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        26                         231
  N1                        14                          90
  N2                        21                          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"
D42V6, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    37  14
  DEL PEAK 17(6Q26) WILD-TYPE 285  48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     37   14
  DEL PEAK 17(6Q26) WILD-TYPE  285   48
   clus
vv  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  0                        37                         285
  1                        14                          48
[1] 2 2
[1] FALSE
D42V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    27  34
  DEL PEAK 17(6Q26) WILD-TYPE 183 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     27   34
  DEL PEAK 17(6Q26) WILD-TYPE  183  199
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        27                         183
  MALE                          34                         199
[1] 2 2
[1] FALSE
D42V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    53   8
  DEL PEAK 17(6Q26) WILD-TYPE 328  52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     53    8
  DEL PEAK 17(6Q26) WILD-TYPE  328   52
                               clus
vv                              DEL PEAK 17(6Q26) MUTATED
  COLON ADENOCARCINOMA                                 53
  COLON MUCINOUS ADENOCARCINOMA                         8
                               clus
vv                              DEL PEAK 17(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                  328
  COLON MUCINOUS ADENOCARCINOMA                          52
[1] 2 2
[1] FALSE
D42V9, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     0  61
  DEL PEAK 17(6Q26) WILD-TYPE   3 379
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      0   61
  DEL PEAK 17(6Q26) WILD-TYPE    3  379
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                          0                           3
  YES                        61                         379
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    40   1   5   6
  DEL PEAK 17(6Q26) WILD-TYPE 276   2  19  19
D42V10, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        40                         276
  R1                         1                           2
  R2                         5                          19
  RX                         6                          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"
D42V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(6Q26) MUTATED                                  1     3
  DEL PEAK 17(6Q26) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED                           5    26
  DEL PEAK 17(6Q26) WILD-TYPE                        49   185
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 17(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   26
                                  clus
vv                                 DEL PEAK 17(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 49
  WHITE                                                    185
[1] 4 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 18(7Q31.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(7Q31.1) MUTATED     9   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 328  91
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           11                           419 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                            2                            91 
$`DEL PEAK 18(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 
       22.03         5.03        15.02        11.38        24.43 

$`DEL PEAK 18(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 
        8.42        31.30         9.70        30.28        70.03 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         5.03                          0.00 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        38.04                        140.38 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        22.03                         20.19 
[1] "5.0 - 38.0 (22.0)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(7Q31.1) MUTATED         2        0        0         5         0
  DEL PEAK 18(7Q31.1) WILD-TYPE      72        1       28       126         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 18(7Q31.1) WILD-TYPE         1        20         11         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(7Q31.1) MUTATED            1        0         1         0
  DEL PEAK 18(7Q31.1) WILD-TYPE         38       43        17         2
D43V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              2                            72
  STAGE IA                             0                             1
  STAGE II                             0                            28
  STAGE IIA                            5                           126
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            11
  STAGE IIIB                           1                            55
  STAGE IIIC                           1                            38
  STAGE IV                             0                            43
  STAGE IVA                            1                            17
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 18(7Q31.1) MUTATED     0   3   9   0
  DEL PEAK 18(7Q31.1) WILD-TYPE  11  75 292  52
D43V4, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            75
  T3                           9                           292
  T4                           0                            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 18(7Q31.1) MUTATED     7   3   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 250 101  79
D43V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                           7                           250
  N1                           3                           101
  N2                           2                            79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    11   1
  DEL PEAK 18(7Q31.1) WILD-TYPE 311  61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     11    1
  DEL PEAK 18(7Q31.1) WILD-TYPE  311   61
   clus
vv  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  0                          11                           311
  1                           1                            61
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     7   5
  DEL PEAK 18(7Q31.1) WILD-TYPE 203 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      7    5
  DEL PEAK 18(7Q31.1) WILD-TYPE  203  228
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           7                           203
  MALE                             5                           228
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    11   1
  DEL PEAK 18(7Q31.1) WILD-TYPE 370  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     11    1
  DEL PEAK 18(7Q31.1) WILD-TYPE  370   59
                               clus
vv                              DEL PEAK 18(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   11
  COLON MUCINOUS ADENOCARCINOMA                           1
                               clus
vv                              DEL PEAK 18(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    370
  COLON MUCINOUS ADENOCARCINOMA                            59
[1] 2 2
[1] FALSE
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     0  12
  DEL PEAK 18(7Q31.1) WILD-TYPE   3 428
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      0   12
  DEL PEAK 18(7Q31.1) WILD-TYPE    3  428
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                            0                             3
  YES                          12                           428
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(7Q31.1) MUTATED    11   0   0   0
  DEL PEAK 18(7Q31.1) WILD-TYPE 305   3  24  25
D43V10, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          11                           305
  R1                           0                             3
  R2                           0                            24
  RX                           0                            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"
D43V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(7Q31.1) MUTATED                                  0     0
  DEL PEAK 18(7Q31.1) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(7Q31.1) MUTATED                           0     9
  DEL PEAK 18(7Q31.1) WILD-TYPE                        54   202
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 18(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK 18(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   54
  WHITE                                                      202
[1] 4 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 19(8P23.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P23.3) MUTATED   141  41
  DEL PEAK 19(8P23.3) WILD-TYPE 196  52
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          182                           248 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                           41                            52 
$`DEL PEAK 19(8P23.3) 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-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       32.91        31.63        29.19        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         9.63         5.03         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3529 TCGA-AA-3531 
        1.02        58.03        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-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 
       13.02        24.00        23.01        19.99        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        6.05         2.01        14.01        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 
       37.05        19.00        36.00        85.05        37.02        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       36.03         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       27.02        29.98         2.01         2.01        34.03         2.01 
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-A02W 
        1.02        33.04        37.02         2.96        39.98        41.00 
TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 
       40.96         4.21         5.79        22.42         0.20        16.31 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       15.75         0.20        17.85        18.84        75.25         5.65 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 
       11.74         3.19         1.94         3.29         0.07         1.35 
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-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 
       13.02        15.02        13.05        11.08        10.06        12.26 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        17.75         1.32        43.27        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G 
      140.38       131.51         6.12        26.47        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 
      117.07        13.38        13.64         1.55        16.31         0.53 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 
        8.35        23.51        74.56        65.85        44.68        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 
       35.93        36.72        36.00        26.43        35.80        91.79 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 
       10.98        19.33         9.93        15.65        12.00         8.42 
TCGA-QL-A97D TCGA-RU-A8FL 
        9.70        30.28 

$`DEL PEAK 19(8P23.3) 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-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        22.52         8.38 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.16        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       24.92         7.04         3.02        35.01        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-3548 TCGA-AA-3554 
        8.05        19.07        19.07        29.00        33.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
        0.92        50.04        47.05        11.01         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04        19.04        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 
        0.00        17.03        10.06         0.00         0.00        32.05 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       53.00        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       26.01        24.00        20.98        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-A02J TCGA-AA-A02O 
       26.01        39.06        51.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.26        19.33        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        5.13        22.36        61.41        49.41         6.77       100.01 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
        0.10        17.56       102.44        40.34        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         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-6172 TCGA-CM-6674 
       16.04        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        12.03        45.40        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 
      119.93        98.24        95.18         8.61        11.11        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        29.59        16.24        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 
       35.41        19.43       107.67        28.21        82.39        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6322 
       53.62        55.04        51.75        45.11        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        26.17        46.75        47.15        52.80        18.18 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        12.79        13.05        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       31.30        70.03 

  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                            0                             0 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                        21.50                         20.07 
[1] "0.0 - 140.4 (21.5)" "0.0 - 139.2 (20.1)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P23.3) MUTATED        25        0        8        41         2
  DEL PEAK 19(8P23.3) WILD-TYPE      49        1       20        90         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P23.3) MUTATED           0        10          6         28
  DEL PEAK 19(8P23.3) WILD-TYPE         1        11          6         28
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P23.3) MUTATED           23       28        10         1
  DEL PEAK 19(8P23.3) WILD-TYPE         16       15         8         1
D44V3, multiclass
            clus
vv           DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  STAGE I                             25                            49
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           41                            90
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                           10                            11
  STAGE IIIA                           6                             6
  STAGE IIIB                          28                            28
  STAGE IIIC                          23                            16
  STAGE IV                            28                            15
  STAGE IVA                           10                             8
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 19(8P23.3) MUTATED     1  31 131  22
  DEL PEAK 19(8P23.3) WILD-TYPE  10  47 170  30
D44V4, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  T1                           1                            10
  T2                          31                            47
  T3                         131                           170
  T4                          22                            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(8P23.3) MUTATED    85  51  48
  DEL PEAK 19(8P23.3) WILD-TYPE 172  53  33
D44V5, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  N0                          85                           172
  N1                          51                            53
  N2                          48                            33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED   124  39
  DEL PEAK 19(8P23.3) WILD-TYPE 198  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED    124   39
  DEL PEAK 19(8P23.3) WILD-TYPE  198   23
   clus
vv  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  0                         124                           198
  1                          39                            23
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED    75 110
  DEL PEAK 19(8P23.3) WILD-TYPE 135 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED     75  110
  DEL PEAK 19(8P23.3) WILD-TYPE  135  123
        clus
vv       DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  FEMALE                          75                           135
  MALE                           110                           123
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED   167  17
  DEL PEAK 19(8P23.3) WILD-TYPE 214  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED    167   17
  DEL PEAK 19(8P23.3) WILD-TYPE  214   43
                               clus
vv                              DEL PEAK 19(8P23.3) MUTATED
  COLON ADENOCARCINOMA                                  167
  COLON MUCINOUS ADENOCARCINOMA                          17
                               clus
vv                              DEL PEAK 19(8P23.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    214
  COLON MUCINOUS ADENOCARCINOMA                            43
[1] 2 2
[1] FALSE
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED     2 183
  DEL PEAK 19(8P23.3) WILD-TYPE   1 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED      2  183
  DEL PEAK 19(8P23.3) WILD-TYPE    1  257
     clus
vv    DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  NO                            2                             1
  YES                         183                           257
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P23.3) MUTATED   126   1  14   6
  DEL PEAK 19(8P23.3) WILD-TYPE 190   2  10  19
D44V10, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  R0                         126                           190
  R1                           1                             2
  R2                          14                            10
  RX                           6                            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"
D44V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P23.3) MUTATED                                  1     3
  DEL PEAK 19(8P23.3) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P23.3) MUTATED                          26    88
  DEL PEAK 19(8P23.3) WILD-TYPE                        28   123
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 19(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                     88
                                  clus
vv                                 DEL PEAK 19(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  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(45) Variable = DEL PEAK 20(8P22) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(8P22) MUTATED   148  49
  DEL PEAK 20(8P22) WILD-TYPE 189  44
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        197                         233 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                         49                          44 
$`DEL PEAK 20(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-3856 
       85.05        37.02        10.06        33.07        36.03         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-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-6715 TCGA-CA-6719 
       11.74         3.19         1.94         3.29         0.07         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
      102.44        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-6172 TCGA-CM-6675 TCGA-CM-6676 
       21.99        13.02        15.02        11.01        13.05        11.08 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       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 
       15.65        12.00         8.42         9.70        30.28 

$`DEL PEAK 20(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-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
        0.00        32.05        53.00        18.05        31.00        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-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-6716 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 
        0.10        17.56        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-6674 TCGA-CM-6677 TCGA-CM-6678 
       14.99        12.99        14.04        12.95        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       10.06        12.03        45.40        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 
       17.85         4.80        17.13        16.14        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         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 
       42.77        29.46        32.98        31.30        70.03 

  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                          0                           0 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                     140.38                      139.17 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                      21.99                       20.02 
[1] "0.0 - 140.4 (22.0)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.3"
D45V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8P22) MUTATED        25        0        9        42         2
  DEL PEAK 20(8P22) WILD-TYPE      49        1       19        89         6
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P22) MUTATED           0        10          8         31
  DEL PEAK 20(8P22) WILD-TYPE         1        11          4         25
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8P22) MUTATED           25       29        14         1
  DEL PEAK 20(8P22) WILD-TYPE         14       14         4         1
D45V3, multiclass
            clus
vv           DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  STAGE I                           25                          49
  STAGE IA                           0                           1
  STAGE II                           9                          19
  STAGE IIA                         42                          89
  STAGE IIB                          2                           6
  STAGE IIC                          0                           1
  STAGE III                         10                          11
  STAGE IIIA                         8                           4
  STAGE IIIB                        31                          25
  STAGE IIIC                        25                          14
  STAGE IV                          29                          14
  STAGE IVA                         14                           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 20(8P22) MUTATED     1  31 142  25
  DEL PEAK 20(8P22) WILD-TYPE  10  47 159  27
D45V4, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  T1                         1                          10
  T2                        31                          47
  T3                       142                         159
  T4                        25                          27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 20(8P22) MUTATED    89  55  54
  DEL PEAK 20(8P22) WILD-TYPE 168  49  27
D45V5, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  N0                        89                         168
  N1                        55                          49
  N2                        54                          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"
D45V6, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   132  44
  DEL PEAK 20(8P22) WILD-TYPE 190  18
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    132   44
  DEL PEAK 20(8P22) WILD-TYPE  190   18
   clus
vv  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  0                       132                         190
  1                        44                          18
[1] 2 2
[1] FALSE
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED    84 115
  DEL PEAK 20(8P22) WILD-TYPE 126 118
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED     84  115
  DEL PEAK 20(8P22) WILD-TYPE  126  118
        clus
vv       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  FEMALE                        84                         126
  MALE                         115                         118
[1] 2 2
[1] FALSE
D45V8, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   181  17
  DEL PEAK 20(8P22) WILD-TYPE 200  43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    181   17
  DEL PEAK 20(8P22) WILD-TYPE  200   43
                               clus
vv                              DEL PEAK 20(8P22) MUTATED
  COLON ADENOCARCINOMA                                181
  COLON MUCINOUS ADENOCARCINOMA                        17
                               clus
vv                              DEL PEAK 20(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                  200
  COLON MUCINOUS ADENOCARCINOMA                          43
[1] 2 2
[1] FALSE
D45V9, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED     2 197
  DEL PEAK 20(8P22) WILD-TYPE   1 243
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED      2  197
  DEL PEAK 20(8P22) WILD-TYPE    1  243
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  NO                          2                           1
  YES                       197                         243
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(8P22) MUTATED   138   1  15   6
  DEL PEAK 20(8P22) WILD-TYPE 178   2   9  19
D45V10, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  R0                       138                         178
  R1                         1                           2
  R2                        15                           9
  RX                         6                          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"
D45V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8P22) MUTATED                                  1     3
  DEL PEAK 20(8P22) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P22) MUTATED                          27   101
  DEL PEAK 20(8P22) WILD-TYPE                        27   110
D45V12, multiclass
                                  clus
vv                                 DEL PEAK 20(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               27
  WHITE                                                  101
                                  clus
vv                                 DEL PEAK 20(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    110
[1] 4 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 21(8Q11.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8Q11.1) MUTATED    23   7
  DEL PEAK 21(8Q11.1) WILD-TYPE 314  86
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           400 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                            7                            86 
$`DEL PEAK 21(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 

$`DEL PEAK 21(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 
       31.30         9.70        30.28        70.03 

  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                       22.060                        20.235 
[1] "0.2 - 131.5 (22.1)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(8Q11.1) MUTATED         2        0        0         9         1
  DEL PEAK 21(8Q11.1) WILD-TYPE      72        1       28       122         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8Q11.1) MUTATED           0         2          1          3
  DEL PEAK 21(8Q11.1) WILD-TYPE         1        19         11         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(8Q11.1) MUTATED            6        3         2         1
  DEL PEAK 21(8Q11.1) WILD-TYPE         33       40        16         1
D46V3, multiclass
            clus
vv           DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  STAGE I                              2                            72
  STAGE IA                             0                             1
  STAGE II                             0                            28
  STAGE IIA                            9                           122
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            2                            19
  STAGE IIIA                           1                            11
  STAGE IIIB                           3                            53
  STAGE IIIC                           6                            33
  STAGE IV                             3                            40
  STAGE IVA                            2                            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 21(8Q11.1) MUTATED     0   3  24   3
  DEL PEAK 21(8Q11.1) WILD-TYPE  11  75 277  49
D46V4, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            75
  T3                          24                           277
  T4                           3                            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 21(8Q11.1) MUTATED    13   8   9
  DEL PEAK 21(8Q11.1) WILD-TYPE 244  96  72
D46V5, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  N0                          13                           244
  N1                           8                            96
  N2                           9                            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"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    20   6
  DEL PEAK 21(8Q11.1) WILD-TYPE 302  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     20    6
  DEL PEAK 21(8Q11.1) WILD-TYPE  302   56
   clus
vv  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  0                          20                           302
  1                           6                            56
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    14  16
  DEL PEAK 21(8Q11.1) WILD-TYPE 196 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     14   16
  DEL PEAK 21(8Q11.1) WILD-TYPE  196  217
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  FEMALE                          14                           196
  MALE                            16                           217
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    26   4
  DEL PEAK 21(8Q11.1) WILD-TYPE 355  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     26    4
  DEL PEAK 21(8Q11.1) WILD-TYPE  355   56
                               clus
vv                              DEL PEAK 21(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                   26
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    355
  COLON MUCINOUS ADENOCARCINOMA                            56
[1] 2 2
[1] FALSE
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED     0  30
  DEL PEAK 21(8Q11.1) WILD-TYPE   3 410
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED      0   30
  DEL PEAK 21(8Q11.1) WILD-TYPE    3  410
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  NO                            0                             3
  YES                          30                           410
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(8Q11.1) MUTATED    24   0   2   0
  DEL PEAK 21(8Q11.1) WILD-TYPE 292   3  22  25
D46V10, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  R0                          24                           292
  R1                           0                             3
  R2                           2                            22
  RX                           0                            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"
D46V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(8Q11.1) MUTATED                                  1     0
  DEL PEAK 21(8Q11.1) WILD-TYPE                                0    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8Q11.1) MUTATED                           6    13
  DEL PEAK 21(8Q11.1) WILD-TYPE                        48   198
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 21(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK 21(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 22(9P21.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED    45  10
  DEL PEAK 22(9P21.3) WILD-TYPE 292  83
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           55                           375 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           10                            83 
$`DEL PEAK 22(9P21.3) MUTATED`
TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 
       43.43        36.53        14.53        29.16        24.16        21.76 
TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3538 TCGA-AA-3553 
       61.84        58.03         6.97        38.99        26.01        24.00 
TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3855 TCGA-AA-3867 
       19.99        37.05        85.05        37.02        32.05        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-A01K TCGA-AA-A01S TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6965 TCGA-AY-4070 
       31.00         1.02        40.96         4.21         0.20        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       17.85         5.65         5.23         3.19         1.94         2.24 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-6169 TCGA-CM-6170 
        3.29         0.26         8.02        22.98        13.02        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6534 
       13.05        11.08        11.01        10.06        20.19        43.27 
TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
        7.53        38.20        14.04        33.67         8.35        82.39 
TCGA-NH-A6GA 
        9.93 

$`DEL PEAK 22(9P21.3) 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-A6-2683 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-A6-4107 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-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        1.02        37.05         1.02        35.01        63.98         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-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       13.02        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        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-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        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-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-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.00        36.03         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-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-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-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        10.88        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09         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-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-6606 TCGA-CA-5255 TCGA-CA-5256 
       12.10       100.01        29.56        11.74         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-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-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.01        12.95        11.08        12.03        45.40        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-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       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-A28A 
      131.51       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 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-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        19.33        19.33        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-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
        9.70        30.28        70.03 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        19.99                         20.61 
[1] "0.2 - 85.0 (20.0)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(9P21.3) MUTATED        10        0        3        15         0
  DEL PEAK 22(9P21.3) WILD-TYPE      64        1       25       116         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P21.3) MUTATED           0         3          3          8
  DEL PEAK 22(9P21.3) WILD-TYPE         1        18          9         48
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(9P21.3) MUTATED            6        6         3         1
  DEL PEAK 22(9P21.3) WILD-TYPE         33       37        15         1
D47V3, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                             10                            64
  STAGE IA                             0                             1
  STAGE II                             3                            25
  STAGE IIA                           15                           116
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           3                             9
  STAGE IIIB                           8                            48
  STAGE IIIC                           6                            33
  STAGE IV                             6                            37
  STAGE IVA                            3                            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 22(9P21.3) MUTATED     2  13  35   9
  DEL PEAK 22(9P21.3) WILD-TYPE   9  65 266  43
D47V4, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T1                           2                             9
  T2                          13                            65
  T3                          35                           266
  T4                           9                            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 22(9P21.3) MUTATED    29  15  14
  DEL PEAK 22(9P21.3) WILD-TYPE 228  89  67
D47V5, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                          29                           228
  N1                          15                            89
  N2                          14                            67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    43  10
  DEL PEAK 22(9P21.3) WILD-TYPE 279  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     43   10
  DEL PEAK 22(9P21.3) WILD-TYPE  279   52
   clus
vv  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  0                          43                           279
  1                          10                            52
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    23  36
  DEL PEAK 22(9P21.3) WILD-TYPE 187 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     23   36
  DEL PEAK 22(9P21.3) WILD-TYPE  187  197
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                          23                           187
  MALE                            36                           197
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    56   3
  DEL PEAK 22(9P21.3) WILD-TYPE 325  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     56    3
  DEL PEAK 22(9P21.3) WILD-TYPE  325   57
                               clus
vv                              DEL PEAK 22(9P21.3) MUTATED
  COLON ADENOCARCINOMA                                   56
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              DEL PEAK 22(9P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    325
  COLON MUCINOUS ADENOCARCINOMA                            57
[1] 2 2
[1] FALSE
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     0  59
  DEL PEAK 22(9P21.3) WILD-TYPE   3 381
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      0   59
  DEL PEAK 22(9P21.3) WILD-TYPE    3  381
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                            0                             3
  YES                          59                           381
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P21.3) MUTATED    41   1   3   3
  DEL PEAK 22(9P21.3) WILD-TYPE 275   2  21  22
D47V10, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                          41                           275
  R1                           1                             2
  R2                           3                            21
  RX                           3                            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"
D47V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9P21.3) MUTATED                                  0     3
  DEL PEAK 22(9P21.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P21.3) MUTATED                           6    27
  DEL PEAK 22(9P21.3) WILD-TYPE                        48   184
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 22(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     27
                                  clus
vv                                 DEL PEAK 22(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      184
[1] 4 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 23(10P15.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10P15.3) MUTATED    59  17
  DEL PEAK 23(10P15.3) WILD-TYPE 278  76
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            76                            354 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            17                             76 
$`DEL PEAK 23(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 
       26.04        46.75        12.79        30.28 

$`DEL PEAK 23(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 

  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                         85.05                         140.38 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                        22.225                         20.155 
[1] "0.2 - 85.0 (22.2)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10P15.3) MUTATED        10        0        6        12         0
  DEL PEAK 23(10P15.3) WILD-TYPE      64        1       22       119         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10P15.3) MUTATED           1         2          4         11
  DEL PEAK 23(10P15.3) WILD-TYPE         0        19          8         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10P15.3) MUTATED            8       16         4         1
  DEL PEAK 23(10P15.3) WILD-TYPE         31       27        14         1
D48V3, multiclass
            clus
vv           DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            12                            119
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            4                              8
  STAGE IIIB                           11                             45
  STAGE IIIC                            8                             31
  STAGE IV                             16                             27
  STAGE IVA                             4                             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 23(10P15.3) MUTATED     1  13  53  10
  DEL PEAK 23(10P15.3) WILD-TYPE  10  65 248  42
D48V4, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  T1                            1                             10
  T2                           13                             65
  T3                           53                            248
  T4                           10                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 23(10P15.3) MUTATED    33  23  21
  DEL PEAK 23(10P15.3) WILD-TYPE 224  81  60
D48V5, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  N0                           33                            224
  N1                           23                             81
  N2                           21                             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"
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    47  21
  DEL PEAK 23(10P15.3) WILD-TYPE 275  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     47   21
  DEL PEAK 23(10P15.3) WILD-TYPE  275   41
   clus
vv  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  0                           47                            275
  1                           21                             41
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    35  42
  DEL PEAK 23(10P15.3) WILD-TYPE 175 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     35   42
  DEL PEAK 23(10P15.3) WILD-TYPE  175  191
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  FEMALE                           35                            175
  MALE                             42                            191
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    69   8
  DEL PEAK 23(10P15.3) WILD-TYPE 312  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     69    8
  DEL PEAK 23(10P15.3) WILD-TYPE  312   52
                               clus
vv                              DEL PEAK 23(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                    69
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 23(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     312
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED     2  75
  DEL PEAK 23(10P15.3) WILD-TYPE   1 365
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED      2   75
  DEL PEAK 23(10P15.3) WILD-TYPE    1  365
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  NO                             2                              1
  YES                           75                            365
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10P15.3) MUTATED    54   0   6   5
  DEL PEAK 23(10P15.3) WILD-TYPE 262   3  18  20
D48V10, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  R0                           54                            262
  R1                            0                              3
  R2                            6                             18
  RX                            5                             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"
D48V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10P15.3) MUTATED                                  0     3
  DEL PEAK 23(10P15.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10P15.3) MUTATED                           7    42
  DEL PEAK 23(10P15.3) WILD-TYPE                        47   169
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 23(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 23(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       169
[1] 4 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 24(10Q21.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10Q21.1) MUTATED    71  21
  DEL PEAK 24(10Q21.1) WILD-TYPE 266  72
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            92                            338 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            21                             72 
$`DEL PEAK 24(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 
       13.05        30.28 

$`DEL PEAK 24(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 
        9.70        70.03 

  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                        117.07                         140.38 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                        21.500                         20.155 
[1] "0.2 - 117.1 (21.5)" "0.0 - 140.4 (20.2)"
[1] "hr=" "1.1"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q21.1) MUTATED        12        0        6        18         0
  DEL PEAK 24(10Q21.1) WILD-TYPE      62        1       22       113         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q21.1) MUTATED           1         2          3         13
  DEL PEAK 24(10Q21.1) WILD-TYPE         0        19          9         43
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q21.1) MUTATED           14       16         5         1
  DEL PEAK 24(10Q21.1) WILD-TYPE         25       27        13         1
D49V3, multiclass
            clus
vv           DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  STAGE I                              12                             62
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            18                            113
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            3                              9
  STAGE IIIB                           13                             43
  STAGE IIIC                           14                             25
  STAGE IV                             16                             27
  STAGE IVA                             5                             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 24(10Q21.1) MUTATED     2  15  66  11
  DEL PEAK 24(10Q21.1) WILD-TYPE   9  63 235  41
D49V4, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  T1                            2                              9
  T2                           15                             63
  T3                           66                            235
  T4                           11                             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 24(10Q21.1) MUTATED    43  25  26
  DEL PEAK 24(10Q21.1) WILD-TYPE 214  79  55
D49V5, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  N0                           43                            214
  N1                           25                             79
  N2                           26                             55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    61  22
  DEL PEAK 24(10Q21.1) WILD-TYPE 261  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     61   22
  DEL PEAK 24(10Q21.1) WILD-TYPE  261   40
   clus
vv  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  0                           61                            261
  1                           22                             40
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    45  49
  DEL PEAK 24(10Q21.1) WILD-TYPE 165 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     45   49
  DEL PEAK 24(10Q21.1) WILD-TYPE  165  184
        clus
vv       DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  FEMALE                           45                            165
  MALE                             49                            184
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    87   7
  DEL PEAK 24(10Q21.1) WILD-TYPE 294  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     87    7
  DEL PEAK 24(10Q21.1) WILD-TYPE  294   53
                               clus
vv                              DEL PEAK 24(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    87
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 24(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     294
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED     2  92
  DEL PEAK 24(10Q21.1) WILD-TYPE   1 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED      2   92
  DEL PEAK 24(10Q21.1) WILD-TYPE    1  348
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  NO                             2                              1
  YES                           92                            348
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10Q21.1) MUTATED    63   1  10   6
  DEL PEAK 24(10Q21.1) WILD-TYPE 253   2  14  19
D49V10, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  R0                           63                            253
  R1                            1                              2
  R2                           10                             14
  RX                            6                             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"
D49V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10Q21.1) MUTATED                                  0     4
  DEL PEAK 24(10Q21.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q21.1) MUTATED                          12    48
  DEL PEAK 24(10Q21.1) WILD-TYPE                        42   163
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      48
                                  clus
vv                                 DEL PEAK 24(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       163
[1] 4 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 25(10Q23.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(10Q23.31) MUTATED    83  21
  DEL PEAK 25(10Q23.31) WILD-TYPE 254  72
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            104                             326 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             21                              72 
$`DEL PEAK 25(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 
       29.46        30.28 

$`DEL PEAK 25(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 
        9.70        70.03 

  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                           0.26                            0.00 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                          21.01                           20.35 
[1] "0.3 - 140.4 (21.0)" "0.0 - 139.2 (20.4)"
[1] "hr=" "1"  
D50V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q23.31) MUTATED        14        1        6        23         0
  DEL PEAK 25(10Q23.31) WILD-TYPE      60        0       22       108         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q23.31) MUTATED           1         4          6         13
  DEL PEAK 25(10Q23.31) WILD-TYPE         0        17          6         43
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q23.31) MUTATED           12       17         5         2
  DEL PEAK 25(10Q23.31) WILD-TYPE         27       26        13         0
D50V3, multiclass
            clus
vv           DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  STAGE I                               14                              60
  STAGE IA                               1                               0
  STAGE II                               6                              22
  STAGE IIA                             23                             108
  STAGE IIB                              0                               8
  STAGE IIC                              1                               0
  STAGE III                              4                              17
  STAGE IIIA                             6                               6
  STAGE IIIB                            13                              43
  STAGE IIIC                            12                              27
  STAGE IV                              17                              26
  STAGE IVA                              5                              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 25(10Q23.31) MUTATED     2  16  74  13
  DEL PEAK 25(10Q23.31) WILD-TYPE   9  62 227  39
D50V4, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  T1                             2                               9
  T2                            16                              62
  T3                            74                             227
  T4                            13                              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 25(10Q23.31) MUTATED    50  30  26
  DEL PEAK 25(10Q23.31) WILD-TYPE 207  74  55
D50V5, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  N0                            50                             207
  N1                            30                              74
  N2                            26                              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    71  24
  DEL PEAK 25(10Q23.31) WILD-TYPE 251  38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     71   24
  DEL PEAK 25(10Q23.31) WILD-TYPE  251   38
   clus
vv  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  0                            71                             251
  1                            24                              38
[1] 2 2
[1] FALSE
D50V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    53  53
  DEL PEAK 25(10Q23.31) WILD-TYPE 157 180
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     53   53
  DEL PEAK 25(10Q23.31) WILD-TYPE  157  180
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  FEMALE                            53                             157
  MALE                              53                             180
[1] 2 2
[1] FALSE
D50V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    96   9
  DEL PEAK 25(10Q23.31) WILD-TYPE 285  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     96    9
  DEL PEAK 25(10Q23.31) WILD-TYPE  285   51
                               clus
vv                              DEL PEAK 25(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                     96
  COLON MUCINOUS ADENOCARCINOMA                             9
                               clus
vv                              DEL PEAK 25(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      285
  COLON MUCINOUS ADENOCARCINOMA                              51
[1] 2 2
[1] FALSE
D50V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED     2 104
  DEL PEAK 25(10Q23.31) WILD-TYPE   1 336
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED      2  104
  DEL PEAK 25(10Q23.31) WILD-TYPE    1  336
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  NO                              2                               1
  YES                           104                             336
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(10Q23.31) MUTATED    75   1  10   5
  DEL PEAK 25(10Q23.31) WILD-TYPE 241   2  14  20
D50V10, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  R0                            75                             241
  R1                             1                               2
  R2                            10                              14
  RX                             5                              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"
D50V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q23.31) MUTATED                                  0     4
  DEL PEAK 25(10Q23.31) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q23.31) MUTATED                          14    55
  DEL PEAK 25(10Q23.31) WILD-TYPE                        40   156
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 25(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     40
  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(51) Variable = DEL PEAK 26(10Q25.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10Q25.2) MUTATED    76  28
  DEL PEAK 26(10Q25.2) WILD-TYPE 261  65
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           104                            326 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                            28                             65 
$`DEL PEAK 26(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 
       13.05        30.28 

$`DEL PEAK 26(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 
        9.70        70.03 

  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                         20.30                          20.35 
[1] "0.2 - 140.4 (20.3)" "0.0 - 139.2 (20.4)"
[1] "hr=" "1.4"
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(10Q25.2) MUTATED        11        0        7        25         0
  DEL PEAK 26(10Q25.2) WILD-TYPE      63        1       21       106         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q25.2) MUTATED           1         6          4         13
  DEL PEAK 26(10Q25.2) WILD-TYPE         0        15          8         43
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(10Q25.2) MUTATED           12       18         5         1
  DEL PEAK 26(10Q25.2) WILD-TYPE         27       25        13         1
D51V3, multiclass
            clus
vv           DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  STAGE I                              11                             63
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            25                            106
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             6                             15
  STAGE IIIA                            4                              8
  STAGE IIIB                           13                             43
  STAGE IIIC                           12                             27
  STAGE IV                             18                             25
  STAGE IVA                             5                             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 26(10Q25.2) MUTATED     2  13  78  13
  DEL PEAK 26(10Q25.2) WILD-TYPE   9  65 223  39
D51V4, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  T1                            2                              9
  T2                           13                             65
  T3                           78                            223
  T4                           13                             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 26(10Q25.2) MUTATED    48  31  27
  DEL PEAK 26(10Q25.2) WILD-TYPE 209  73  54
D51V5, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  N0                           48                            209
  N1                           31                             73
  N2                           27                             54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    72  24
  DEL PEAK 26(10Q25.2) WILD-TYPE 250  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     72   24
  DEL PEAK 26(10Q25.2) WILD-TYPE  250   38
   clus
vv  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  0                           72                            250
  1                           24                             38
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    50  56
  DEL PEAK 26(10Q25.2) WILD-TYPE 160 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     50   56
  DEL PEAK 26(10Q25.2) WILD-TYPE  160  177
        clus
vv       DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  FEMALE                           50                            160
  MALE                             56                            177
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    97   9
  DEL PEAK 26(10Q25.2) WILD-TYPE 284  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     97    9
  DEL PEAK 26(10Q25.2) WILD-TYPE  284   51
                               clus
vv                              DEL PEAK 26(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                    97
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              DEL PEAK 26(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     284
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED     2 104
  DEL PEAK 26(10Q25.2) WILD-TYPE   1 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED      2  104
  DEL PEAK 26(10Q25.2) WILD-TYPE    1  336
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  NO                             2                              1
  YES                          104                            336
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10Q25.2) MUTATED    72   1  11   5
  DEL PEAK 26(10Q25.2) WILD-TYPE 244   2  13  20
D51V10, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  R0                           72                            244
  R1                            1                              2
  R2                           11                             13
  RX                            5                             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"
D51V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(10Q25.2) MUTATED                                  0     3
  DEL PEAK 26(10Q25.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10Q25.2) MUTATED                          13    53
  DEL PEAK 26(10Q25.2) WILD-TYPE                        41   158
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 26(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       158
[1] 4 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 27(12P13.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.2) MUTATED    41  18
  DEL PEAK 27(12P13.2) WILD-TYPE 296  75
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            59                            371 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            18                             75 
$`DEL PEAK 27(12P13.2) 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-3548 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3688 
       33.99        13.02        78.08         2.01        50.04        19.00 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A01F 
       31.07        17.03        24.03         2.01        50.99        32.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-4070 
       33.04         2.96         5.79        22.42        16.44        16.31 
TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 
       11.74         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-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 
        1.32        15.12         7.53        13.41        11.38        13.32 
TCGA-DM-A1D8 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 
       12.59        13.38        11.11        16.24        65.85        36.72 
TCGA-G4-6317 TCGA-NH-A50U TCGA-NH-A8F7 TCGA-QL-A97D TCGA-RU-A8FL 
       36.00        10.98        13.05         9.70        30.28 

$`DEL PEAK 27(12P13.2) 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-A6-2678 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-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 
       12.99         0.99        14.01        21.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-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-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04        19.04 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
       15.95        38.99        36.95        37.02        14.93         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        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-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72        27.42        10.88         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09         0.95        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-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-D5-6930 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-A1D9 TCGA-DM-A1DA 
       38.20       130.65        92.75        49.91       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        95.18         8.61        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
        6.18        35.87         1.55        16.31        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       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-G4-6304 
        8.35        82.39        23.51        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-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 
       29.46        32.98         8.42        31.30        70.03 

  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                         78.08                         140.38 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                         16.24                          21.14 
[1] "0.1 - 78.1 (16.2)"  "0.0 - 140.4 (21.1)"
[1] "hr=" "1.8"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.2) MUTATED        10        0        2         9         1
  DEL PEAK 27(12P13.2) WILD-TYPE      64        1       26       122         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.2) MUTATED           0         2          1          9
  DEL PEAK 27(12P13.2) WILD-TYPE         1        19         11         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(12P13.2) MUTATED           10       10         3         0
  DEL PEAK 27(12P13.2) WILD-TYPE         29       33        15         2
D52V3, multiclass
            clus
vv           DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              2                             26
  STAGE IIA                             9                            122
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             2                             19
  STAGE IIIA                            1                             11
  STAGE IIIB                            9                             47
  STAGE IIIC                           10                             29
  STAGE IV                             10                             33
  STAGE IVA                             3                             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 27(12P13.2) MUTATED     2   9  41   7
  DEL PEAK 27(12P13.2) WILD-TYPE   9  69 260  45
D52V4, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  T1                            2                              9
  T2                            9                             69
  T3                           41                            260
  T4                            7                             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 27(12P13.2) MUTATED    26  19  14
  DEL PEAK 27(12P13.2) WILD-TYPE 231  85  67
D52V5, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  N0                           26                            231
  N1                           19                             85
  N2                           14                             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    35  13
  DEL PEAK 27(12P13.2) WILD-TYPE 287  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     35   13
  DEL PEAK 27(12P13.2) WILD-TYPE  287   49
   clus
vv  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  0                           35                            287
  1                           13                             49
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    29  30
  DEL PEAK 27(12P13.2) WILD-TYPE 181 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     29   30
  DEL PEAK 27(12P13.2) WILD-TYPE  181  203
        clus
vv       DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  FEMALE                           29                            181
  MALE                             30                            203
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    57   2
  DEL PEAK 27(12P13.2) WILD-TYPE 324  58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     57    2
  DEL PEAK 27(12P13.2) WILD-TYPE  324   58
                               clus
vv                              DEL PEAK 27(12P13.2) MUTATED
  COLON ADENOCARCINOMA                                    57
  COLON MUCINOUS ADENOCARCINOMA                            2
                               clus
vv                              DEL PEAK 27(12P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     324
  COLON MUCINOUS ADENOCARCINOMA                             58
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED     0  59
  DEL PEAK 27(12P13.2) WILD-TYPE   3 381
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED      0   59
  DEL PEAK 27(12P13.2) WILD-TYPE    3  381
     clus
vv    DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  NO                             0                              3
  YES                           59                            381
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.2) MUTATED    41   1   4   4
  DEL PEAK 27(12P13.2) WILD-TYPE 275   2  20  21
D52V10, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  R0                           41                            275
  R1                            1                              2
  R2                            4                             20
  RX                            4                             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"
D52V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12P13.2) MUTATED                                  0     2
  DEL PEAK 27(12P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12P13.2) MUTATED                          10    32
  DEL PEAK 27(12P13.2) WILD-TYPE                        44   179
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 27(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       179
[1] 4 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 28(13Q14.13) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(13Q14.13) MUTATED    14   4
  DEL PEAK 28(13Q14.13) WILD-TYPE 323  89
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                             18                             412 
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                              4                              89 
$`DEL PEAK 28(13Q14.13) MUTATED`
TCGA-A6-2685 TCGA-AA-3524 TCGA-AA-3548 TCGA-AA-3556 TCGA-AA-3664 TCGA-AA-3875 
       37.25        36.03        33.99        23.01        54.02        18.05 
TCGA-AA-3968 TCGA-AY-6196 TCGA-AZ-4315 TCGA-AZ-4681 TCGA-AZ-6607 TCGA-CA-5797 
       21.99         0.20        58.39        83.80         3.19         3.29 
TCGA-CM-6675 TCGA-DM-A1D8 TCGA-F4-6461 TCGA-F4-6704 TCGA-G4-6626 TCGA-RU-A8FL 
       13.05        12.59        11.11         1.55        46.75        30.28 

$`DEL PEAK 28(13Q14.13) 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-A6-2686 TCGA-A6-3807 
       45.60        13.94        16.57        37.05        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-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3530 
       24.03        37.05         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-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        21.01        13.02        24.00        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-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       20.98        34.03         2.01        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        38.04         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       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-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-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       10.88         0.20        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        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-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-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-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-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-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-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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        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-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       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-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-F4-6805 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-WS-AB45 
        8.42        31.30         9.70        70.03 

  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                          83.80                          140.38 
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                         22.500                          20.235 
[1] "0.2 - 83.8 (22.5)"  "0.0 - 140.4 (20.2)"
[1] "hr=" "1"  
D53V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(13Q14.13) MUTATED         4        0        2         5         0
  DEL PEAK 28(13Q14.13) WILD-TYPE      70        1       26       126         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(13Q14.13) MUTATED           0         0          0          1
  DEL PEAK 28(13Q14.13) WILD-TYPE         1        21         12         55
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(13Q14.13) MUTATED            4        1         0         1
  DEL PEAK 28(13Q14.13) WILD-TYPE         35       42        18         1
D53V3, multiclass
            clus
vv           DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  STAGE I                                4                              70
  STAGE IA                               0                               1
  STAGE II                               2                              26
  STAGE IIA                              5                             126
  STAGE IIB                              0                               8
  STAGE IIC                              0                               1
  STAGE III                              0                              21
  STAGE IIIA                             0                              12
  STAGE IIIB                             1                              55
  STAGE IIIC                             4                              35
  STAGE IV                               1                              42
  STAGE IVA                              0                              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 28(13Q14.13) MUTATED     1   3  13   2
  DEL PEAK 28(13Q14.13) WILD-TYPE  10  75 288  50
D53V4, multiclass
    clus
vv   DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  T1                             1                              10
  T2                             3                              75
  T3                            13                             288
  T4                             2                              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 28(13Q14.13) MUTATED    11   1   7
  DEL PEAK 28(13Q14.13) WILD-TYPE 246 103  74
D53V5, multiclass
    clus
vv   DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  N0                            11                             246
  N1                             1                             103
  N2                             7                              74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED    12   2
  DEL PEAK 28(13Q14.13) WILD-TYPE 310  60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED     12    2
  DEL PEAK 28(13Q14.13) WILD-TYPE  310   60
   clus
vv  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  0                            12                             310
  1                             2                              60
[1] 2 2
[1] FALSE
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED     8  11
  DEL PEAK 28(13Q14.13) WILD-TYPE 202 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED      8   11
  DEL PEAK 28(13Q14.13) WILD-TYPE  202  222
        clus
vv       DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  FEMALE                             8                             202
  MALE                              11                             222
[1] 2 2
[1] FALSE
D53V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED    16   2
  DEL PEAK 28(13Q14.13) WILD-TYPE 365  58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED     16    2
  DEL PEAK 28(13Q14.13) WILD-TYPE  365   58
                               clus
vv                              DEL PEAK 28(13Q14.13) MUTATED
  COLON ADENOCARCINOMA                                     16
  COLON MUCINOUS ADENOCARCINOMA                             2
                               clus
vv                              DEL PEAK 28(13Q14.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      365
  COLON MUCINOUS ADENOCARCINOMA                              58
[1] 2 2
[1] FALSE
D53V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED     0  19
  DEL PEAK 28(13Q14.13) WILD-TYPE   3 421
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED      0   19
  DEL PEAK 28(13Q14.13) WILD-TYPE    3  421
     clus
vv    DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  NO                              0                               3
  YES                            19                             421
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(13Q14.13) MUTATED    16   0   0   1
  DEL PEAK 28(13Q14.13) WILD-TYPE 300   3  24  24
D53V10, multiclass
    clus
vv   DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  R0                            16                             300
  R1                             0                               3
  R2                             0                              24
  RX                             1                              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"
D53V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(13Q14.13) MUTATED                                  1     1
  DEL PEAK 28(13Q14.13) WILD-TYPE                                0    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(13Q14.13) MUTATED                           3     8
  DEL PEAK 28(13Q14.13) WILD-TYPE                        51   203
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 28(13Q14.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    3
  WHITE                                                        8
                                  clus
vv                                 DEL PEAK 28(13Q14.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     51
  WHITE                                                        203
[1] 4 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 29(14Q31.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(14Q31.1) MUTATED   111  30
  DEL PEAK 29(14Q31.1) WILD-TYPE 226  63
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                           141                            289 
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                            30                             63 
$`DEL PEAK 29(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-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 
       34.03        12.99        13.02        23.01        13.94        19.99 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 
       19.00        85.05        10.06        25.02        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 
       17.03        31.07        17.03        24.03        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       12.99         2.01        21.99        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       26.01        24.00         7.96        38.04        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       14.99        21.99        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 
       26.01         2.96         2.01        40.96         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       27.42        16.44        14.50         0.95        15.75         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 
       17.85        18.84        75.25         1.41         5.65        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 
       29.56         5.23         1.94         3.06         2.14         0.07 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 
        0.26        49.08         2.01        25.02         8.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        13.02        15.02        13.05        11.08 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 
       10.06        45.40        12.26        13.51        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 
       15.12        14.30        13.41        11.38        38.20        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F 
      140.38         7.50       131.51        14.04       119.93        35.97 
TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 
       13.38        29.59        33.67        13.25         0.53         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 
       13.05        12.00        30.28 

$`DEL PEAK 29(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-3543 
        8.05         0.00        29.00        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
       54.02         0.92        47.05        11.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04        19.04        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        14.93         0.00 
TCGA-AA-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-3869 TCGA-AA-3870 TCGA-AA-3877 
        0.99        31.07        53.00        27.02        29.98        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
        2.01        13.05        25.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C 
       18.05         4.01         0.99        17.03        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       10.88         0.20         0.46         0.92        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82        17.26        19.33        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.25         3.29         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        19.59        11.51        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB 
       24.43       130.65        92.75        49.91        12.59        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        26.47        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
       16.24        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-G4-6310 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 
       70.03 

  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                         19.07                          21.14 
[1] "0.1 - 140.4 (19.1)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(14Q31.1) MUTATED        21        0        7        36         1
  DEL PEAK 29(14Q31.1) WILD-TYPE      53        1       21        95         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q31.1) MUTATED           0         9          4         19
  DEL PEAK 29(14Q31.1) WILD-TYPE         1        12          8         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(14Q31.1) MUTATED           14       20        10         1
  DEL PEAK 29(14Q31.1) WILD-TYPE         25       23         8         1
D54V3, multiclass
            clus
vv           DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  STAGE I                              21                             53
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            36                             95
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             9                             12
  STAGE IIIA                            4                              8
  STAGE IIIB                           19                             37
  STAGE IIIC                           14                             25
  STAGE IV                             20                             23
  STAGE IVA                            10                              8
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(14Q31.1) MUTATED     6  22 102  15
  DEL PEAK 29(14Q31.1) WILD-TYPE   5  56 199  37
D54V4, multiclass
    clus
vv   DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  T1                            6                              5
  T2                           22                             56
  T3                          102                            199
  T4                           15                             37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 29(14Q31.1) MUTATED    71  41  33
  DEL PEAK 29(14Q31.1) WILD-TYPE 186  63  48
D54V5, multiclass
    clus
vv   DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  N0                           71                            186
  N1                           41                             63
  N2                           33                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED    98  31
  DEL PEAK 29(14Q31.1) WILD-TYPE 224  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED     98   31
  DEL PEAK 29(14Q31.1) WILD-TYPE  224   31
   clus
vv  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  0                           98                            224
  1                           31                             31
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED    65  80
  DEL PEAK 29(14Q31.1) WILD-TYPE 145 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED     65   80
  DEL PEAK 29(14Q31.1) WILD-TYPE  145  153
        clus
vv       DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  FEMALE                           65                            145
  MALE                             80                            153
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED   138   5
  DEL PEAK 29(14Q31.1) WILD-TYPE 243  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED    138    5
  DEL PEAK 29(14Q31.1) WILD-TYPE  243   55
                               clus
vv                              DEL PEAK 29(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   138
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 29(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     243
  COLON MUCINOUS ADENOCARCINOMA                             55
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED     0 145
  DEL PEAK 29(14Q31.1) WILD-TYPE   3 295
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED      0  145
  DEL PEAK 29(14Q31.1) WILD-TYPE    3  295
     clus
vv    DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  NO                             0                              3
  YES                          145                            295
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(14Q31.1) MUTATED    97   0  11   8
  DEL PEAK 29(14Q31.1) WILD-TYPE 219   3  13  17
D54V10, multiclass
    clus
vv   DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  R0                           97                            219
  R1                            0                              3
  R2                           11                             13
  RX                            8                             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"
D54V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(14Q31.1) MUTATED                                  0     4
  DEL PEAK 29(14Q31.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(14Q31.1) MUTATED                          17    67
  DEL PEAK 29(14Q31.1) WILD-TYPE                        37   144
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  17
  WHITE                                                      67
                                  clus
vv                                 DEL PEAK 29(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       144
[1] 4 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 30(15Q11.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(15Q11.2) MUTATED   132  35
  DEL PEAK 30(15Q11.2) WILD-TYPE 205  58
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           167                            263 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                            35                             58 
$`DEL PEAK 30(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 
       19.33        12.79        29.46         9.70        30.28 

$`DEL PEAK 30(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 
       42.77        32.98         8.42        31.30        70.03 

  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                          0.26                           0.00 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                         20.61                          20.02 
[1] "0.3 - 140.4 (20.6)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(15Q11.2) MUTATED        28        0        7        40         2
  DEL PEAK 30(15Q11.2) WILD-TYPE      46        1       21        91         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(15Q11.2) MUTATED           0         6          8         23
  DEL PEAK 30(15Q11.2) WILD-TYPE         1        15          4         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(15Q11.2) MUTATED           20       22        11         2
  DEL PEAK 30(15Q11.2) WILD-TYPE         19       21         7         0
D55V3, multiclass
            clus
vv           DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  STAGE I                              28                             46
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             91
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            8                              4
  STAGE IIIB                           23                             33
  STAGE IIIC                           20                             19
  STAGE IV                             22                             21
  STAGE IVA                            11                              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 30(15Q11.2) MUTATED     5  30 117  21
  DEL PEAK 30(15Q11.2) WILD-TYPE   6  48 184  31
D55V4, multiclass
    clus
vv   DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  T1                            5                              6
  T2                           30                             48
  T3                          117                            184
  T4                           21                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 30(15Q11.2) MUTATED    85  49  39
  DEL PEAK 30(15Q11.2) WILD-TYPE 172  55  42
D55V5, multiclass
    clus
vv   DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  N0                           85                            172
  N1                           49                             55
  N2                           39                             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"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED   116  35
  DEL PEAK 30(15Q11.2) WILD-TYPE 206  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED    116   35
  DEL PEAK 30(15Q11.2) WILD-TYPE  206   27
   clus
vv  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  0                          116                            206
  1                           35                             27
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED    80  93
  DEL PEAK 30(15Q11.2) WILD-TYPE 130 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED     80   93
  DEL PEAK 30(15Q11.2) WILD-TYPE  130  140
        clus
vv       DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  FEMALE                           80                            130
  MALE                             93                            140
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED   155  16
  DEL PEAK 30(15Q11.2) WILD-TYPE 226  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED    155   16
  DEL PEAK 30(15Q11.2) WILD-TYPE  226   44
                               clus
vv                              DEL PEAK 30(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   155
  COLON MUCINOUS ADENOCARCINOMA                           16
                               clus
vv                              DEL PEAK 30(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     226
  COLON MUCINOUS ADENOCARCINOMA                             44
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED     3 170
  DEL PEAK 30(15Q11.2) WILD-TYPE   0 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED      3  170
  DEL PEAK 30(15Q11.2) WILD-TYPE    0  270
     clus
vv    DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  NO                             3                              0
  YES                          170                            270
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(15Q11.2) MUTATED   120   1  12   7
  DEL PEAK 30(15Q11.2) WILD-TYPE 196   2  12  18
D55V10, multiclass
    clus
vv   DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  R0                          120                            196
  R1                            1                              2
  R2                           12                             12
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(15Q11.2) MUTATED                                  1     3
  DEL PEAK 30(15Q11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(15Q11.2) MUTATED                          18    89
  DEL PEAK 30(15Q11.2) WILD-TYPE                        36   122
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 30(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK 30(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       122
[1] 4 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 31(15Q15.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q15.2) MUTATED   130  33
  DEL PEAK 31(15Q15.2) WILD-TYPE 207  60
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           163                            267 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                            33                             60 
$`DEL PEAK 31(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 
       30.28 

$`DEL PEAK 31(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 
        8.42        31.30        70.03 

  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                         20.61                          20.02 
[1] "0.2 - 140.4 (20.6)" "0.0 - 139.2 (20.0)"
[1] "hr=" "1.2"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q15.2) MUTATED        29        0        7        37         2
  DEL PEAK 31(15Q15.2) WILD-TYPE      45        1       21        94         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q15.2) MUTATED           0         6          6         22
  DEL PEAK 31(15Q15.2) WILD-TYPE         1        15          6         34
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q15.2) MUTATED           19       24        10         2
  DEL PEAK 31(15Q15.2) WILD-TYPE         20       19         8         0
D56V3, multiclass
            clus
vv           DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  STAGE I                              29                             45
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            37                             94
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              6
  STAGE IIIB                           22                             34
  STAGE IIIC                           19                             20
  STAGE IV                             24                             19
  STAGE IVA                            10                              8
  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(15Q15.2) MUTATED     5  30 113  20
  DEL PEAK 31(15Q15.2) WILD-TYPE   6  48 188  32
D56V4, multiclass
    clus
vv   DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  T1                            5                              6
  T2                           30                             48
  T3                          113                            188
  T4                           20                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 31(15Q15.2) MUTATED    82  50  36
  DEL PEAK 31(15Q15.2) WILD-TYPE 175  54  45
D56V5, multiclass
    clus
vv   DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  N0                           82                            175
  N1                           50                             54
  N2                           36                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED   108  36
  DEL PEAK 31(15Q15.2) WILD-TYPE 214  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED    108   36
  DEL PEAK 31(15Q15.2) WILD-TYPE  214   26
   clus
vv  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  0                          108                            214
  1                           36                             26
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED    78  90
  DEL PEAK 31(15Q15.2) WILD-TYPE 132 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED     78   90
  DEL PEAK 31(15Q15.2) WILD-TYPE  132  143
        clus
vv       DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  FEMALE                           78                            132
  MALE                             90                            143
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED   151  15
  DEL PEAK 31(15Q15.2) WILD-TYPE 230  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED    151   15
  DEL PEAK 31(15Q15.2) WILD-TYPE  230   45
                               clus
vv                              DEL PEAK 31(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                   151
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 31(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     230
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED     3 165
  DEL PEAK 31(15Q15.2) WILD-TYPE   0 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED      3  165
  DEL PEAK 31(15Q15.2) WILD-TYPE    0  275
     clus
vv    DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  NO                             3                              0
  YES                          165                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q15.2) MUTATED   118   1  12   6
  DEL PEAK 31(15Q15.2) WILD-TYPE 198   2  12  19
D56V10, multiclass
    clus
vv   DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  R0                          118                            198
  R1                            1                              2
  R2                           12                             12
  RX                            6                             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"
D56V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(15Q15.2) MUTATED                                  1     2
  DEL PEAK 31(15Q15.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(15Q15.2) MUTATED                          20    86
  DEL PEAK 31(15Q15.2) WILD-TYPE                        34   125
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 31(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       125
[1] 4 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 32(15Q21.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q21.1) MUTATED   129  31
  DEL PEAK 32(15Q21.1) WILD-TYPE 208  62
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           160                            270 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                            31                             62 
$`DEL PEAK 32(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 
       12.79        29.46         9.70        30.28 

$`DEL PEAK 32(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 

  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                        21.385                         19.625 
[1] "0.0 - 140.4 (21.4)" "0.0 - 139.2 (19.6)"
[1] "hr=" "1.2"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q21.1) MUTATED        26        0        7        40         3
  DEL PEAK 32(15Q21.1) WILD-TYPE      48        1       21        91         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q21.1) MUTATED           0         6          6         20
  DEL PEAK 32(15Q21.1) WILD-TYPE         1        15          6         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q21.1) MUTATED           18       23        10         2
  DEL PEAK 32(15Q21.1) WILD-TYPE         21       20         8         0
D57V3, multiclass
            clus
vv           DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  STAGE I                              26                             48
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             91
  STAGE IIB                             3                              5
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              6
  STAGE IIIB                           20                             36
  STAGE IIIC                           18                             21
  STAGE IV                             23                             20
  STAGE IVA                            10                              8
  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(15Q21.1) MUTATED     4  28 112  21
  DEL PEAK 32(15Q21.1) WILD-TYPE   7  50 189  31
D57V4, multiclass
    clus
vv   DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  T1                            4                              7
  T2                           28                             50
  T3                          112                            189
  T4                           21                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 32(15Q21.1) MUTATED    83  47  35
  DEL PEAK 32(15Q21.1) WILD-TYPE 174  57  46
D57V5, multiclass
    clus
vv   DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  N0                           83                            174
  N1                           47                             57
  N2                           35                             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"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED   107  35
  DEL PEAK 32(15Q21.1) WILD-TYPE 215  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED    107   35
  DEL PEAK 32(15Q21.1) WILD-TYPE  215   27
   clus
vv  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  0                          107                            215
  1                           35                             27
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED    75  90
  DEL PEAK 32(15Q21.1) WILD-TYPE 135 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED     75   90
  DEL PEAK 32(15Q21.1) WILD-TYPE  135  143
        clus
vv       DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  FEMALE                           75                            135
  MALE                             90                            143
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED   149  15
  DEL PEAK 32(15Q21.1) WILD-TYPE 232  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED    149   15
  DEL PEAK 32(15Q21.1) WILD-TYPE  232   45
                               clus
vv                              DEL PEAK 32(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                   149
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 32(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     232
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED     3 162
  DEL PEAK 32(15Q21.1) WILD-TYPE   0 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED      3  162
  DEL PEAK 32(15Q21.1) WILD-TYPE    0  278
     clus
vv    DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  NO                             3                              0
  YES                          162                            278
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q21.1) MUTATED   116   0  12   6
  DEL PEAK 32(15Q21.1) WILD-TYPE 200   3  12  19
D57V10, multiclass
    clus
vv   DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  R0                          116                            200
  R1                            0                              3
  R2                           12                             12
  RX                            6                             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"
D57V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q21.1) MUTATED                                  1     2
  DEL PEAK 32(15Q21.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q21.1) MUTATED                          16    84
  DEL PEAK 32(15Q21.1) WILD-TYPE                        38   127
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      84
                                  clus
vv                                 DEL PEAK 32(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       127
[1] 4 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 33(15Q22.33) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(15Q22.33) MUTATED   121  32
  DEL PEAK 33(15Q22.33) WILD-TYPE 216  61
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            153                             277 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                             32                              61 
$`DEL PEAK 33(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 
        8.42         9.70        30.28 

$`DEL PEAK 33(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 
       70.03 

  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                          19.99                           20.98 
[1] "0.2 - 140.4 (20.0)" "0.0 - 139.2 (21.0)"
[1] "hr=" "1.1"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q22.33) MUTATED        23        0        6        37         2
  DEL PEAK 33(15Q22.33) WILD-TYPE      51        1       22        94         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q22.33) MUTATED           0         5          7         19
  DEL PEAK 33(15Q22.33) WILD-TYPE         1        16          5         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q22.33) MUTATED           20       22        11         1
  DEL PEAK 33(15Q22.33) WILD-TYPE         19       21         7         1
D58V3, multiclass
            clus
vv           DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  STAGE I                               23                              51
  STAGE IA                               0                               1
  STAGE II                               6                              22
  STAGE IIA                             37                              94
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             7                               5
  STAGE IIIB                            19                              37
  STAGE IIIC                            20                              19
  STAGE IV                              22                              21
  STAGE IVA                             11                               7
  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 33(15Q22.33) MUTATED     5  23 110  19
  DEL PEAK 33(15Q22.33) WILD-TYPE   6  55 191  33
D58V4, multiclass
    clus
vv   DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  T1                             5                               6
  T2                            23                              55
  T3                           110                             191
  T4                            19                              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 33(15Q22.33) MUTATED    76  44  37
  DEL PEAK 33(15Q22.33) WILD-TYPE 181  60  44
D58V5, multiclass
    clus
vv   DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  N0                            76                             181
  N1                            44                              60
  N2                            37                              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED   100  34
  DEL PEAK 33(15Q22.33) WILD-TYPE 222  28
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED    100   34
  DEL PEAK 33(15Q22.33) WILD-TYPE  222   28
   clus
vv  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  0                           100                             222
  1                            34                              28
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED    72  85
  DEL PEAK 33(15Q22.33) WILD-TYPE 138 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED     72   85
  DEL PEAK 33(15Q22.33) WILD-TYPE  138  148
        clus
vv       DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  FEMALE                            72                             138
  MALE                              85                             148
[1] 2 2
[1] FALSE
D58V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED   141  14
  DEL PEAK 33(15Q22.33) WILD-TYPE 240  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED    141   14
  DEL PEAK 33(15Q22.33) WILD-TYPE  240   46
                               clus
vv                              DEL PEAK 33(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                    141
  COLON MUCINOUS ADENOCARCINOMA                            14
                               clus
vv                              DEL PEAK 33(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      240
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
D58V9, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED     3 154
  DEL PEAK 33(15Q22.33) WILD-TYPE   0 286
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED      3  154
  DEL PEAK 33(15Q22.33) WILD-TYPE    0  286
     clus
vv    DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  NO                              3                               0
  YES                           154                             286
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(15Q22.33) MUTATED   109   1  11   6
  DEL PEAK 33(15Q22.33) WILD-TYPE 207   2  13  19
D58V10, multiclass
    clus
vv   DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  R0                           109                             207
  R1                             1                               2
  R2                            11                              13
  RX                             6                              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"
D58V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q22.33) MUTATED                                  1     2
  DEL PEAK 33(15Q22.33) WILD-TYPE                                0     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q22.33) MUTATED                          17    84
  DEL PEAK 33(15Q22.33) WILD-TYPE                        37   127
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                       84
                                  clus
vv                                 DEL PEAK 33(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     37
  WHITE                                                        127
[1] 4 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 34(16P13.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16P13.3) MUTATED    34  18
  DEL PEAK 34(16P13.3) WILD-TYPE 303  75
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            52                            378 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            18                             75 
$`DEL PEAK 34(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 
       18.18        10.98        42.77        30.28 

$`DEL PEAK 34(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 

  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                         61.84                         140.38 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                        19.185                         20.515 
[1] "0.2 - 61.8 (19.2)"  "0.0 - 140.4 (20.5)"
[1] "hr=" "2"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(16P13.3) MUTATED         3        0        3        16         2
  DEL PEAK 34(16P13.3) WILD-TYPE      71        1       25       115         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(16P13.3) MUTATED           0         0          0          9
  DEL PEAK 34(16P13.3) WILD-TYPE         1        21         12         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(16P13.3) MUTATED            9        6         5         0
  DEL PEAK 34(16P13.3) WILD-TYPE         30       37        13         2
D59V3, multiclass
            clus
vv           DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  STAGE I                               3                             71
  STAGE IA                              0                              1
  STAGE II                              3                             25
  STAGE IIA                            16                            115
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             0                             21
  STAGE IIIA                            0                             12
  STAGE IIIB                            9                             47
  STAGE IIIC                            9                             30
  STAGE IV                              6                             37
  STAGE IVA                             5                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(16P13.3) MUTATED     0   3  44   7
  DEL PEAK 34(16P13.3) WILD-TYPE  11  75 257  45
D59V4, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  T1                            0                             11
  T2                            3                             75
  T3                           44                            257
  T4                            7                             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 34(16P13.3) MUTATED    25  15  14
  DEL PEAK 34(16P13.3) WILD-TYPE 232  89  67
D59V5, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  N0                           25                            232
  N1                           15                             89
  N2                           14                             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    34  11
  DEL PEAK 34(16P13.3) WILD-TYPE 288  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     34   11
  DEL PEAK 34(16P13.3) WILD-TYPE  288   51
   clus
vv  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  0                           34                            288
  1                           11                             51
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    24  30
  DEL PEAK 34(16P13.3) WILD-TYPE 186 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     24   30
  DEL PEAK 34(16P13.3) WILD-TYPE  186  203
        clus
vv       DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  FEMALE                           24                            186
  MALE                             30                            203
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    47   7
  DEL PEAK 34(16P13.3) WILD-TYPE 334  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     47    7
  DEL PEAK 34(16P13.3) WILD-TYPE  334   53
                               clus
vv                              DEL PEAK 34(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                    47
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 34(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     334
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED     0  54
  DEL PEAK 34(16P13.3) WILD-TYPE   3 386
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED      0   54
  DEL PEAK 34(16P13.3) WILD-TYPE    3  386
     clus
vv    DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  NO                             0                              3
  YES                           54                            386
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16P13.3) MUTATED    40   1   3   1
  DEL PEAK 34(16P13.3) WILD-TYPE 276   2  21  24
D59V10, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  R0                           40                            276
  R1                            1                              2
  R2                            3                             21
  RX                            1                             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"
D59V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(16P13.3) MUTATED                                  0     0
  DEL PEAK 34(16P13.3) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16P13.3) MUTATED                          10    27
  DEL PEAK 34(16P13.3) WILD-TYPE                        44   184
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 34(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK 34(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       184
[1] 4 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 35(16Q23.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16Q23.1) MUTATED    41  16
  DEL PEAK 35(16Q23.1) WILD-TYPE 296  77
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            57                            373 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            16                             77 
$`DEL PEAK 35(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 
       10.98        31.30        30.28 

$`DEL PEAK 35(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 
       70.03 

  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                          0.92                           0.00 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                         53.00                         140.38 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                         18.18                          20.61 
[1] "0.9 - 53.0 (18.2)"  "0.0 - 140.4 (20.6)"
[1] "hr=" "1.9"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(16Q23.1) MUTATED        10        0        5        17         2
  DEL PEAK 35(16Q23.1) WILD-TYPE      64        1       23       114         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(16Q23.1) MUTATED           0         3          0          8
  DEL PEAK 35(16Q23.1) WILD-TYPE         1        18         12         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(16Q23.1) MUTATED            3        6         4         0
  DEL PEAK 35(16Q23.1) WILD-TYPE         36       37        14         2
D60V3, multiclass
            clus
vv           DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            17                            114
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            0                             12
  STAGE IIIB                            8                             48
  STAGE IIIC                            3                             36
  STAGE IV                              6                             37
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 35(16Q23.1) MUTATED     0  10  39   9
  DEL PEAK 35(16Q23.1) WILD-TYPE  11  68 262  43
D60V4, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  T1                            0                             11
  T2                           10                             68
  T3                           39                            262
  T4                            9                             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 35(16Q23.1) MUTATED    36  14   8
  DEL PEAK 35(16Q23.1) WILD-TYPE 221  90  73
D60V5, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  N0                           36                            221
  N1                           14                             90
  N2                            8                             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"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    40  10
  DEL PEAK 35(16Q23.1) WILD-TYPE 282  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     40   10
  DEL PEAK 35(16Q23.1) WILD-TYPE  282   52
   clus
vv  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  0                           40                            282
  1                           10                             52
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    31  27
  DEL PEAK 35(16Q23.1) WILD-TYPE 179 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     31   27
  DEL PEAK 35(16Q23.1) WILD-TYPE  179  206
        clus
vv       DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  FEMALE                           31                            179
  MALE                             27                            206
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    48  10
  DEL PEAK 35(16Q23.1) WILD-TYPE 333  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     48   10
  DEL PEAK 35(16Q23.1) WILD-TYPE  333   50
                               clus
vv                              DEL PEAK 35(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                    48
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK 35(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     333
  COLON MUCINOUS ADENOCARCINOMA                             50
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED     0  58
  DEL PEAK 35(16Q23.1) WILD-TYPE   3 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED      0   58
  DEL PEAK 35(16Q23.1) WILD-TYPE    3  382
     clus
vv    DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  NO                             0                              3
  YES                           58                            382
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16Q23.1) MUTATED    40   0   2   4
  DEL PEAK 35(16Q23.1) WILD-TYPE 276   3  22  21
D60V10, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  R0                           40                            276
  R1                            0                              3
  R2                            2                             22
  RX                            4                             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"
D60V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(16Q23.1) MUTATED                                  0     2
  DEL PEAK 35(16Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(16Q23.1) MUTATED                          11    22
  DEL PEAK 35(16Q23.1) WILD-TYPE                        43   189
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 35(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 35(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       189
[1] 4 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 36(17P12) MUTATION ANALYSIS
D61V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(17P12) MUTATED   187  54
  DEL PEAK 36(17P12) WILD-TYPE 150  39
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         241                          189 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                          54                           39 
$`DEL PEAK 36(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 
       30.28 

$`DEL PEAK 36(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 
       19.33        31.30        70.03 

  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                        0.07                         0.00 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                      140.38                       135.65 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                       21.01                        20.02 
[1] "0.1 - 140.4 (21.0)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.2"
D61V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(17P12) MUTATED        36        0       13        55         1
  DEL PEAK 36(17P12) WILD-TYPE      38        1       15        76         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(17P12) MUTATED           1        12         11         35
  DEL PEAK 36(17P12) WILD-TYPE         0         9          1         21
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(17P12) MUTATED           30       33        13         2
  DEL PEAK 36(17P12) WILD-TYPE          9       10         5         0
D61V3, multiclass
            clus
vv           DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  STAGE I                            36                           38
  STAGE IA                            0                            1
  STAGE II                           13                           15
  STAGE IIA                          55                           76
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                          12                            9
  STAGE IIIA                         11                            1
  STAGE IIIB                         35                           21
  STAGE IIIC                         30                            9
  STAGE IV                           33                           10
  STAGE IVA                          13                            5
  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 36(17P12) MUTATED     7  41 170  30
  DEL PEAK 36(17P12) WILD-TYPE   4  37 131  22
D61V4, multiclass
    clus
vv   DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  T1                          7                            4
  T2                         41                           37
  T3                        170                          131
  T4                         30                           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
  DEL PEAK 36(17P12) MUTATED   118  70  59
  DEL PEAK 36(17P12) WILD-TYPE 139  34  22
D61V5, multiclass
    clus
vv   DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  N0                        118                          139
  N1                         70                           34
  N2                         59                           22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED   169  48
  DEL PEAK 36(17P12) WILD-TYPE 153  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED    169   48
  DEL PEAK 36(17P12) WILD-TYPE  153   14
   clus
vv  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  0                        169                          153
  1                         48                           14
[1] 2 2
[1] FALSE
D61V7, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED   111 137
  DEL PEAK 36(17P12) WILD-TYPE  99  96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED    111  137
  DEL PEAK 36(17P12) WILD-TYPE   99   96
        clus
vv       DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  FEMALE                        111                           99
  MALE                          137                           96
[1] 2 2
[1] FALSE
D61V8, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED   229  17
  DEL PEAK 36(17P12) WILD-TYPE 152  43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED    229   17
  DEL PEAK 36(17P12) WILD-TYPE  152   43
                               clus
vv                              DEL PEAK 36(17P12) MUTATED
  COLON ADENOCARCINOMA                                 229
  COLON MUCINOUS ADENOCARCINOMA                         17
                               clus
vv                              DEL PEAK 36(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   152
  COLON MUCINOUS ADENOCARCINOMA                           43
[1] 2 2
[1] FALSE
D61V9, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED     3 245
  DEL PEAK 36(17P12) WILD-TYPE   0 195
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED      3  245
  DEL PEAK 36(17P12) WILD-TYPE    0  195
     clus
vv    DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  NO                           3                            0
  YES                        245                          195
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 36(17P12) MUTATED   173   1  17  10
  DEL PEAK 36(17P12) WILD-TYPE 143   2   7  15
D61V10, multiclass
    clus
vv   DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  R0                        173                          143
  R1                          1                            2
  R2                         17                            7
  RX                         10                           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"
D61V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(17P12) MUTATED                                  0     6
  DEL PEAK 36(17P12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(17P12) MUTATED                          32   119
  DEL PEAK 36(17P12) WILD-TYPE                        22    92
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 36(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                32
  WHITE                                                   119
                                  clus
vv                                 DEL PEAK 36(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                      92
[1] 4 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 37(17Q24.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(17Q24.3) MUTATED    48  20
  DEL PEAK 37(17Q24.3) WILD-TYPE 289  73
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            68                            362 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            20                             73 
$`DEL PEAK 37(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 
       42.77         9.70 

$`DEL PEAK 37(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 
       30.28        70.03 

  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                         20.50                          20.35 
[1] "0.2 - 140.4 (20.5)" "0.0 - 139.2 (20.4)"
[1] "hr=" "1.6"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(17Q24.3) MUTATED        10        0        4        10         0
  DEL PEAK 37(17Q24.3) WILD-TYPE      64        1       24       121         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17Q24.3) MUTATED           0         3          3          7
  DEL PEAK 37(17Q24.3) WILD-TYPE         1        18          9         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(17Q24.3) MUTATED           11       10         7         1
  DEL PEAK 37(17Q24.3) WILD-TYPE         28       33        11         1
D62V3, multiclass
            clus
vv           DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            10                            121
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            3                              9
  STAGE IIIB                            7                             49
  STAGE IIIC                           11                             28
  STAGE IV                             10                             33
  STAGE IVA                             7                             11
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(17Q24.3) MUTATED     0  12  45  12
  DEL PEAK 37(17Q24.3) WILD-TYPE  11  66 256  40
D62V4, multiclass
    clus
vv   DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  T1                            0                             11
  T2                           12                             66
  T3                           45                            256
  T4                           12                             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 37(17Q24.3) MUTATED    27  23  19
  DEL PEAK 37(17Q24.3) WILD-TYPE 230  81  62
D62V5, multiclass
    clus
vv   DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  N0                           27                            230
  N1                           23                             81
  N2                           19                             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"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED    39  18
  DEL PEAK 37(17Q24.3) WILD-TYPE 283  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED     39   18
  DEL PEAK 37(17Q24.3) WILD-TYPE  283   44
   clus
vv  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  0                           39                            283
  1                           18                             44
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED    29  40
  DEL PEAK 37(17Q24.3) WILD-TYPE 181 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED     29   40
  DEL PEAK 37(17Q24.3) WILD-TYPE  181  193
        clus
vv       DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  FEMALE                           29                            181
  MALE                             40                            193
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED    59  10
  DEL PEAK 37(17Q24.3) WILD-TYPE 322  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED     59   10
  DEL PEAK 37(17Q24.3) WILD-TYPE  322   50
                               clus
vv                              DEL PEAK 37(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                    59
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK 37(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     322
  COLON MUCINOUS ADENOCARCINOMA                             50
[1] 2 2
[1] FALSE
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED     0  69
  DEL PEAK 37(17Q24.3) WILD-TYPE   3 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED      0   69
  DEL PEAK 37(17Q24.3) WILD-TYPE    3  371
     clus
vv    DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  NO                             0                              3
  YES                           69                            371
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(17Q24.3) MUTATED    43   0   6   4
  DEL PEAK 37(17Q24.3) WILD-TYPE 273   3  18  21
D62V10, multiclass
    clus
vv   DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  R0                           43                            273
  R1                            0                              3
  R2                            6                             18
  RX                            4                             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"
D62V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(17Q24.3) MUTATED                                  1     2
  DEL PEAK 37(17Q24.3) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(17Q24.3) MUTATED                           9    34
  DEL PEAK 37(17Q24.3) WILD-TYPE                        45   177
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 37(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 37(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    45
  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(63) Variable = DEL PEAK 38(18P11.31) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 38(18P11.31) MUTATED   188  47
  DEL PEAK 38(18P11.31) WILD-TYPE 149  46
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            235                             195 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                             47                              46 
$`DEL PEAK 38(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 
       30.28 

$`DEL PEAK 38(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 
       29.46        31.30        70.03 

  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                           0.07                            0.00 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                         140.38                          135.65 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                          20.98                           20.02 
[1] "0.1 - 140.4 (21.0)" "0.0 - 135.7 (20.0)"
[1] "hr=" "1.1"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(18P11.31) MUTATED        36        0       10        65         2
  DEL PEAK 38(18P11.31) WILD-TYPE      38        1       18        66         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(18P11.31) MUTATED           1         9          8         33
  DEL PEAK 38(18P11.31) WILD-TYPE         0        12          4         23
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(18P11.31) MUTATED           22       32        16         1
  DEL PEAK 38(18P11.31) WILD-TYPE         17       11         2         1
D63V3, multiclass
            clus
vv           DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  STAGE I                               36                              38
  STAGE IA                               0                               1
  STAGE II                              10                              18
  STAGE IIA                             65                              66
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                              9                              12
  STAGE IIIA                             8                               4
  STAGE IIIB                            33                              23
  STAGE IIIC                            22                              17
  STAGE IV                              32                              11
  STAGE IVA                             16                               2
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 38(18P11.31) MUTATED     7  41 163  30
  DEL PEAK 38(18P11.31) WILD-TYPE   4  37 138  22
D63V4, multiclass
    clus
vv   DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  T1                             7                               4
  T2                            41                              37
  T3                           163                             138
  T4                            30                              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
  DEL PEAK 38(18P11.31) MUTATED   126  67  47
  DEL PEAK 38(18P11.31) WILD-TYPE 131  37  34
D63V5, multiclass
    clus
vv   DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  N0                           126                             131
  N1                            67                              37
  N2                            47                              34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED   161  49
  DEL PEAK 38(18P11.31) WILD-TYPE 161  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED    161   49
  DEL PEAK 38(18P11.31) WILD-TYPE  161   13
   clus
vv  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  0                           161                             161
  1                            49                              13
[1] 2 2
[1] FALSE
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED   112 129
  DEL PEAK 38(18P11.31) WILD-TYPE  98 104
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED    112  129
  DEL PEAK 38(18P11.31) WILD-TYPE   98  104
        clus
vv       DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  FEMALE                           112                              98
  MALE                             129                             104
[1] 2 2
[1] FALSE
D63V8, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED   229  10
  DEL PEAK 38(18P11.31) WILD-TYPE 152  50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED    229   10
  DEL PEAK 38(18P11.31) WILD-TYPE  152   50
                               clus
vv                              DEL PEAK 38(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                    229
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              DEL PEAK 38(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      152
  COLON MUCINOUS ADENOCARCINOMA                              50
[1] 2 2
[1] FALSE
D63V9, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED     3 238
  DEL PEAK 38(18P11.31) WILD-TYPE   0 202
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED      3  238
  DEL PEAK 38(18P11.31) WILD-TYPE    0  202
     clus
vv    DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  NO                              3                               0
  YES                           238                             202
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 38(18P11.31) MUTATED   169   0  18  11
  DEL PEAK 38(18P11.31) WILD-TYPE 147   3   6  14
D63V10, multiclass
    clus
vv   DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  R0                           169                             147
  R1                             0                               3
  R2                            18                               6
  RX                            11                              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"
D63V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(18P11.31) MUTATED                                  1     6
  DEL PEAK 38(18P11.31) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(18P11.31) MUTATED                          32   116
  DEL PEAK 38(18P11.31) WILD-TYPE                        22    95
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 38(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      116
                                  clus
vv                                 DEL PEAK 38(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                         95
[1] 4 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 39(18Q12.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(18Q12.2) MUTATED   207  55
  DEL PEAK 39(18Q12.2) WILD-TYPE 130  38
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           262                            168 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            55                             38 
$`DEL PEAK 39(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 
       32.98         8.42         9.70        30.28 

$`DEL PEAK 39(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 

  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                        20.445                         20.270 
[1] "0.1 - 140.4 (20.4)" "0.0 - 135.7 (20.3)"
[1] "hr=" "1.1"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18Q12.2) MUTATED        38        0       15        69         2
  DEL PEAK 39(18Q12.2) WILD-TYPE      36        1       13        62         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q12.2) MUTATED           1        11         11         37
  DEL PEAK 39(18Q12.2) WILD-TYPE         0        10          1         19
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(18Q12.2) MUTATED           27       35        14         1
  DEL PEAK 39(18Q12.2) WILD-TYPE         12        8         4         1
D64V3, multiclass
            clus
vv           DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  STAGE I                              38                             36
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            69                             62
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           11                              1
  STAGE IIIB                           37                             19
  STAGE IIIC                           27                             12
  STAGE IV                             35                              8
  STAGE IVA                            14                              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 39(18Q12.2) MUTATED     6  45 187  30
  DEL PEAK 39(18Q12.2) WILD-TYPE   5  33 114  22
D64V4, multiclass
    clus
vv   DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  T1                            6                              5
  T2                           45                             33
  T3                          187                            114
  T4                           30                             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
  DEL PEAK 39(18Q12.2) MUTATED   136  73  58
  DEL PEAK 39(18Q12.2) WILD-TYPE 121  31  23
D64V5, multiclass
    clus
vv   DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  N0                          136                            121
  N1                           73                             31
  N2                           58                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED   187  50
  DEL PEAK 39(18Q12.2) WILD-TYPE 135  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED    187   50
  DEL PEAK 39(18Q12.2) WILD-TYPE  135   12
   clus
vv  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  0                          187                            135
  1                           50                             12
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED   120 148
  DEL PEAK 39(18Q12.2) WILD-TYPE  90  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED    120  148
  DEL PEAK 39(18Q12.2) WILD-TYPE   90   85
        clus
vv       DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  FEMALE                          120                             90
  MALE                            148                             85
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED   252  15
  DEL PEAK 39(18Q12.2) WILD-TYPE 129  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED    252   15
  DEL PEAK 39(18Q12.2) WILD-TYPE  129   45
                               clus
vv                              DEL PEAK 39(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                   252
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 39(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     129
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED     3 265
  DEL PEAK 39(18Q12.2) WILD-TYPE   0 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED      3  265
  DEL PEAK 39(18Q12.2) WILD-TYPE    0  175
     clus
vv    DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  NO                             3                              0
  YES                          265                            175
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(18Q12.2) MUTATED   189   1  18  11
  DEL PEAK 39(18Q12.2) WILD-TYPE 127   2   6  14
D64V10, multiclass
    clus
vv   DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  R0                          189                            127
  R1                            1                              2
  R2                           18                              6
  RX                           11                             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"
D64V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(18Q12.2) MUTATED                                  1     6
  DEL PEAK 39(18Q12.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(18Q12.2) MUTATED                          32   132
  DEL PEAK 39(18Q12.2) WILD-TYPE                        22    79
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 39(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  32
  WHITE                                                     132
                                  clus
vv                                 DEL PEAK 39(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                        79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = DEL PEAK 40(18Q21.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(18Q21.2) MUTATED   217  59
  DEL PEAK 40(18Q21.2) WILD-TYPE 120  34
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           276                            154 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            59                             34 
$`DEL PEAK 40(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 

$`DEL PEAK 40(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 
       15.65        29.46        31.30        70.03 

  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                          0.07                           0.00 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                        20.795                         20.070 
[1] "0.1 - 140.4 (20.8)" "0.0 - 135.7 (20.1)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18Q21.2) MUTATED        40        0       16        71         2
  DEL PEAK 40(18Q21.2) WILD-TYPE      34        1       12        60         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q21.2) MUTATED           1        11         11         40
  DEL PEAK 40(18Q21.2) WILD-TYPE         0        10          1         16
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18Q21.2) MUTATED           30       37        15         2
  DEL PEAK 40(18Q21.2) WILD-TYPE          9        6         3         0
D65V3, multiclass
            clus
vv           DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  STAGE I                              40                             34
  STAGE IA                              0                              1
  STAGE II                             16                             12
  STAGE IIA                            71                             60
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           11                              1
  STAGE IIIB                           40                             16
  STAGE IIIC                           30                              9
  STAGE IV                             37                              6
  STAGE IVA                            15                              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 40(18Q21.2) MUTATED     7  46 195  34
  DEL PEAK 40(18Q21.2) WILD-TYPE   4  32 106  18
D65V4, multiclass
    clus
vv   DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  T1                            7                              4
  T2                           46                             32
  T3                          195                            106
  T4                           34                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 40(18Q21.2) MUTATED   141  77  63
  DEL PEAK 40(18Q21.2) WILD-TYPE 116  27  18
D65V5, multiclass
    clus
vv   DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  N0                          141                            116
  N1                           77                             27
  N2                           63                             18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED   195  54
  DEL PEAK 40(18Q21.2) WILD-TYPE 127   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED    195   54
  DEL PEAK 40(18Q21.2) WILD-TYPE  127    8
   clus
vv  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  0                          195                            127
  1                           54                              8
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED   124 158
  DEL PEAK 40(18Q21.2) WILD-TYPE  86  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED    124  158
  DEL PEAK 40(18Q21.2) WILD-TYPE   86   75
        clus
vv       DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  FEMALE                          124                             86
  MALE                            158                             75
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED   264  17
  DEL PEAK 40(18Q21.2) WILD-TYPE 117  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED    264   17
  DEL PEAK 40(18Q21.2) WILD-TYPE  117   43
                               clus
vv                              DEL PEAK 40(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   264
  COLON MUCINOUS ADENOCARCINOMA                           17
                               clus
vv                              DEL PEAK 40(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     117
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED     3 279
  DEL PEAK 40(18Q21.2) WILD-TYPE   0 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED      3  279
  DEL PEAK 40(18Q21.2) WILD-TYPE    0  161
     clus
vv    DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  NO                             3                              0
  YES                          279                            161
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(18Q21.2) MUTATED   198   1  18  11
  DEL PEAK 40(18Q21.2) WILD-TYPE 118   2   6  14
D65V10, multiclass
    clus
vv   DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  R0                          198                            118
  R1                            1                              2
  R2                           18                              6
  RX                           11                             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"
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(18Q21.2) MUTATED                                  1     6
  DEL PEAK 40(18Q21.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18Q21.2) MUTATED                          36   141
  DEL PEAK 40(18Q21.2) WILD-TYPE                        18    70
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     141
                                  clus
vv                                 DEL PEAK 40(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    18
  WHITE                                                        70
[1] 4 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 41(19P13.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(19P13.3) MUTATED    44  17
  DEL PEAK 41(19P13.3) WILD-TYPE 293  76
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            61                            369 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                            17                             76 
$`DEL PEAK 41(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 
       30.28 

$`DEL PEAK 41(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 
       31.30         9.70        70.03 

  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE 
                         23.01                          20.02 
[1] "0.0 - 131.5 (23.0)" "0.0 - 140.4 (20.0)"
[1] "hr=" "1.3"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(19P13.3) MUTATED         8        0        1        11         0
  DEL PEAK 41(19P13.3) WILD-TYPE      66        1       27       120         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(19P13.3) MUTATED           0         4          3          6
  DEL PEAK 41(19P13.3) WILD-TYPE         1        17          9         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(19P13.3) MUTATED           12       10         4         1
  DEL PEAK 41(19P13.3) WILD-TYPE         27       33        14         1
D66V3, multiclass
            clus
vv           DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  STAGE I                               8                             66
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            11                            120
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            3                              9
  STAGE IIIB                            6                             50
  STAGE IIIC                           12                             27
  STAGE IV                             10                             33
  STAGE IVA                             4                             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 41(19P13.3) MUTATED     1   9  43   9
  DEL PEAK 41(19P13.3) WILD-TYPE  10  69 258  43
D66V4, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  T1                            1                             10
  T2                            9                             69
  T3                           43                            258
  T4                            9                             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 41(19P13.3) MUTATED    22  16  24
  DEL PEAK 41(19P13.3) WILD-TYPE 235  88  57
D66V5, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  N0                           22                            235
  N1                           16                             88
  N2                           24                             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"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    38  15
  DEL PEAK 41(19P13.3) WILD-TYPE 284  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     38   15
  DEL PEAK 41(19P13.3) WILD-TYPE  284   47
   clus
vv  DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  0                           38                            284
  1                           15                             47
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    25  37
  DEL PEAK 41(19P13.3) WILD-TYPE 185 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     25   37
  DEL PEAK 41(19P13.3) WILD-TYPE  185  196
        clus
vv       DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  FEMALE                           25                            185
  MALE                             37                            196
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED    56   5
  DEL PEAK 41(19P13.3) WILD-TYPE 325  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED     56    5
  DEL PEAK 41(19P13.3) WILD-TYPE  325   55
                               clus
vv                              DEL PEAK 41(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                    56
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 41(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     325
  COLON MUCINOUS ADENOCARCINOMA                             55
[1] 2 2
[1] FALSE
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(19P13.3) MUTATED     1  61
  DEL PEAK 41(19P13.3) WILD-TYPE   2 379
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(19P13.3) MUTATED      1   61
  DEL PEAK 41(19P13.3) WILD-TYPE    2  379
     clus
vv    DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  NO                             1                              2
  YES                           61                            379
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(19P13.3) MUTATED    40   1   7   3
  DEL PEAK 41(19P13.3) WILD-TYPE 276   2  17  22
D66V10, multiclass
    clus
vv   DEL PEAK 41(19P13.3) MUTATED DEL PEAK 41(19P13.3) WILD-TYPE
  R0                           40                            276
  R1                            1                              2
  R2                            7                             17
  RX                            3                             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"
D66V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(19P13.3) MUTATED                                  0     1
  DEL PEAK 41(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(19P13.3) MUTATED                           7    25
  DEL PEAK 41(19P13.3) WILD-TYPE                        47   186
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 41(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK 41(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    47
  WHITE                                                       186
[1] 4 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 42(20P12.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(20P12.1) MUTATED    67  15
  DEL PEAK 42(20P12.1) WILD-TYPE 270  78
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            82                            348 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                            15                             78 
$`DEL PEAK 42(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 
       19.33        12.00         8.42        30.28 

$`DEL PEAK 42(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 

  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE 
                        24.015                         19.625 
[1] "0.2 - 131.5 (24.0)" "0.0 - 140.4 (19.6)"
[1] "hr=" "1.4"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(20P12.1) MUTATED        10        0        6        22         0
  DEL PEAK 42(20P12.1) WILD-TYPE      64        1       22       109         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(20P12.1) MUTATED           1         4          2         15
  DEL PEAK 42(20P12.1) WILD-TYPE         0        17         10         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(20P12.1) MUTATED           10        8         4         0
  DEL PEAK 42(20P12.1) WILD-TYPE         29       35        14         2
D67V3, multiclass
            clus
vv           DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  STAGE I                              10                             64
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            22                            109
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            2                             10
  STAGE IIIB                           15                             41
  STAGE IIIC                           10                             29
  STAGE IV                              8                             35
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(20P12.1) MUTATED     1  11  62   9
  DEL PEAK 42(20P12.1) WILD-TYPE  10  67 239  43
D67V4, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  T1                            1                             10
  T2                           11                             67
  T3                           62                            239
  T4                            9                             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 42(20P12.1) MUTATED    42  23  18
  DEL PEAK 42(20P12.1) WILD-TYPE 215  81  63
D67V5, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  N0                           42                            215
  N1                           23                             81
  N2                           18                             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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    62  12
  DEL PEAK 42(20P12.1) WILD-TYPE 260  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     62   12
  DEL PEAK 42(20P12.1) WILD-TYPE  260   50
   clus
vv  DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  0                           62                            260
  1                           12                             50
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    40  43
  DEL PEAK 42(20P12.1) WILD-TYPE 170 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     40   43
  DEL PEAK 42(20P12.1) WILD-TYPE  170  190
        clus
vv       DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  FEMALE                           40                            170
  MALE                             43                            190
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED    77   6
  DEL PEAK 42(20P12.1) WILD-TYPE 304  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED     77    6
  DEL PEAK 42(20P12.1) WILD-TYPE  304   54
                               clus
vv                              DEL PEAK 42(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    77
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              DEL PEAK 42(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     304
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(20P12.1) MUTATED     0  83
  DEL PEAK 42(20P12.1) WILD-TYPE   3 357
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(20P12.1) MUTATED      0   83
  DEL PEAK 42(20P12.1) WILD-TYPE    3  357
     clus
vv    DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  NO                             0                              3
  YES                           83                            357
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(20P12.1) MUTATED    55   0   3   2
  DEL PEAK 42(20P12.1) WILD-TYPE 261   3  21  23
D67V10, multiclass
    clus
vv   DEL PEAK 42(20P12.1) MUTATED DEL PEAK 42(20P12.1) WILD-TYPE
  R0                           55                            261
  R1                            0                              3
  R2                            3                             21
  RX                            2                             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"
D67V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(20P12.1) MUTATED                                  0     0
  DEL PEAK 42(20P12.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(20P12.1) MUTATED                           9    45
  DEL PEAK 42(20P12.1) WILD-TYPE                        45   166
D67V12, multiclass
                                  clus
vv                                 DEL PEAK 42(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 42(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    45
  WHITE                                                       166
[1] 4 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 43(21Q11.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(21Q11.2) MUTATED   102  29
  DEL PEAK 43(21Q11.2) WILD-TYPE 235  64
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           131                            299 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                            29                             64 
$`DEL PEAK 43(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 
       46.75        18.18         9.93        13.05        42.77 

$`DEL PEAK 43(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 
        8.42        31.30         9.70        30.28        70.03 

  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE 
                         19.07                          21.37 
[1] "0.2 - 140.4 (19.1)" "0.0 - 139.2 (21.4)"
[1] "hr=" "1.2"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(21Q11.2) MUTATED        23        0        8        36         1
  DEL PEAK 43(21Q11.2) WILD-TYPE      51        1       20        95         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(21Q11.2) MUTATED           0         4          5         15
  DEL PEAK 43(21Q11.2) WILD-TYPE         1        17          7         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(21Q11.2) MUTATED           17       20         4         0
  DEL PEAK 43(21Q11.2) WILD-TYPE         22       23        14         2
D68V3, multiclass
            clus
vv           DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  STAGE I                              23                             51
  STAGE IA                              0                              1
  STAGE II                              8                             20
  STAGE IIA                            36                             95
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            5                              7
  STAGE IIIB                           15                             41
  STAGE IIIC                           17                             22
  STAGE IV                             20                             23
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 43(21Q11.2) MUTATED     6  23  91  17
  DEL PEAK 43(21Q11.2) WILD-TYPE   5  55 210  35
D68V4, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  T1                            6                              5
  T2                           23                             55
  T3                           91                            210
  T4                           17                             35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 43(21Q11.2) MUTATED    70  32  35
  DEL PEAK 43(21Q11.2) WILD-TYPE 187  72  46
D68V5, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  N0                           70                            187
  N1                           32                             72
  N2                           35                             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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    92  24
  DEL PEAK 43(21Q11.2) WILD-TYPE 230  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     92   24
  DEL PEAK 43(21Q11.2) WILD-TYPE  230   38
   clus
vv  DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  0                           92                            230
  1                           24                             38
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED    64  73
  DEL PEAK 43(21Q11.2) WILD-TYPE 146 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED     64   73
  DEL PEAK 43(21Q11.2) WILD-TYPE  146  160
        clus
vv       DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  FEMALE                           64                            146
  MALE                             73                            160
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED   127   8
  DEL PEAK 43(21Q11.2) WILD-TYPE 254  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED    127    8
  DEL PEAK 43(21Q11.2) WILD-TYPE  254   52
                               clus
vv                              DEL PEAK 43(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   127
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 43(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     254
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(21Q11.2) MUTATED     2 135
  DEL PEAK 43(21Q11.2) WILD-TYPE   1 305
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(21Q11.2) MUTATED      2  135
  DEL PEAK 43(21Q11.2) WILD-TYPE    1  305
     clus
vv    DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  NO                             2                              1
  YES                          135                            305
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(21Q11.2) MUTATED    94   1  10   7
  DEL PEAK 43(21Q11.2) WILD-TYPE 222   2  14  18
D68V10, multiclass
    clus
vv   DEL PEAK 43(21Q11.2) MUTATED DEL PEAK 43(21Q11.2) WILD-TYPE
  R0                           94                            222
  R1                            1                              2
  R2                           10                             14
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(21Q11.2) MUTATED                                  1     4
  DEL PEAK 43(21Q11.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(21Q11.2) MUTATED                          15    66
  DEL PEAK 43(21Q11.2) WILD-TYPE                        39   145
D68V12, multiclass
                                  clus
vv                                 DEL PEAK 43(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 43(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    39
  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(69) Variable = DEL PEAK 44(22Q13.32) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(22Q13.32) MUTATED   116  37
  DEL PEAK 44(22Q13.32) WILD-TYPE 221  56
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            153                             277 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                             37                              56 
$`DEL PEAK 44(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 
       29.46         9.70        30.28 

$`DEL PEAK 44(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 
       70.03 

  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE 
                          18.18                           21.14 
[1] "0.2 - 140.4 (18.2)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.4"
D69V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 44(22Q13.32) MUTATED        19        0        7        39         1
  DEL PEAK 44(22Q13.32) WILD-TYPE      55        1       21        92         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(22Q13.32) MUTATED           0         7          7         19
  DEL PEAK 44(22Q13.32) WILD-TYPE         1        14          5         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(22Q13.32) MUTATED           21       24         8         0
  DEL PEAK 44(22Q13.32) WILD-TYPE         18       19        10         2
D69V3, multiclass
            clus
vv           DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  STAGE I                               19                              55
  STAGE IA                               0                               1
  STAGE II                               7                              21
  STAGE IIA                             39                              92
  STAGE IIB                              1                               7
  STAGE IIC                              0                               1
  STAGE III                              7                              14
  STAGE IIIA                             7                               5
  STAGE IIIB                            19                              37
  STAGE IIIC                            21                              18
  STAGE IV                              24                              19
  STAGE IVA                              8                              10
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 44(22Q13.32) MUTATED     3  24 107  22
  DEL PEAK 44(22Q13.32) WILD-TYPE   8  54 194  30
D69V4, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  T1                             3                               8
  T2                            24                              54
  T3                           107                             194
  T4                            22                              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 44(22Q13.32) MUTATED    71  45  40
  DEL PEAK 44(22Q13.32) WILD-TYPE 186  59  41
D69V5, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  N0                            71                             186
  N1                            45                              59
  N2                            40                              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"
D69V6, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   103  32
  DEL PEAK 44(22Q13.32) WILD-TYPE 219  30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    103   32
  DEL PEAK 44(22Q13.32) WILD-TYPE  219   30
   clus
vv  DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  0                           103                             219
  1                            32                              30
[1] 2 2
[1] FALSE
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED    72  84
  DEL PEAK 44(22Q13.32) WILD-TYPE 138 149
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED     72   84
  DEL PEAK 44(22Q13.32) WILD-TYPE  138  149
        clus
vv       DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  FEMALE                            72                             138
  MALE                              84                             149
[1] 2 2
[1] FALSE
D69V8, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED   145  11
  DEL PEAK 44(22Q13.32) WILD-TYPE 236  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED    145   11
  DEL PEAK 44(22Q13.32) WILD-TYPE  236   49
                               clus
vv                              DEL PEAK 44(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                    145
  COLON MUCINOUS ADENOCARCINOMA                            11
                               clus
vv                              DEL PEAK 44(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                      236
  COLON MUCINOUS ADENOCARCINOMA                              49
[1] 2 2
[1] FALSE
D69V9, binary
                                 cls
clus                                0   1
  DEL PEAK 44(22Q13.32) MUTATED     1 155
  DEL PEAK 44(22Q13.32) WILD-TYPE   2 285
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(22Q13.32) MUTATED      1  155
  DEL PEAK 44(22Q13.32) WILD-TYPE    2  285
     clus
vv    DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  NO                              1                               2
  YES                           155                             285
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 44(22Q13.32) MUTATED   105   1  10  11
  DEL PEAK 44(22Q13.32) WILD-TYPE 211   2  14  14
D69V10, multiclass
    clus
vv   DEL PEAK 44(22Q13.32) MUTATED DEL PEAK 44(22Q13.32) WILD-TYPE
  R0                           105                             211
  R1                             1                               2
  R2                            10                              14
  RX                            11                              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"
D69V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(22Q13.32) MUTATED                                  1     4
  DEL PEAK 44(22Q13.32) WILD-TYPE                                0     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(22Q13.32) MUTATED                          22    69
  DEL PEAK 44(22Q13.32) WILD-TYPE                        32   142
D69V12, multiclass
                                  clus
vv                                 DEL PEAK 44(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                       69
                                  clus
vv                                 DEL PEAK 44(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     32
  WHITE                                                        142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
