[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/10005863/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/10013691/transformed.cor.cli.txt"

nPatients in clinical file=441, in cluster file=438, common to both=430
[1]  69 430
[1] "AMP PEAK  1(2Q33.1) MUTATION ANALYSIS"
[1] 3
  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 
                           84                           346 
[1] "AMP PEAK  2(5P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           82                           348 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           82                           348 
[1] "AMP PEAK  3(5Q22.3) MUTATION ANALYSIS"
[1] 3
  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 
                           43                           387 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           91                           339 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           91                           339 
[1] "AMP PEAK  5(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                           151                            279 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                           151                            279 
[1] "AMP PEAK  6(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                           179                            251 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                           179                            251 
[1] "AMP PEAK  7(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                          224                           206 
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                          224                           206 
[1] "AMP PEAK  8(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           247                            183 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           247                            183 
[1] "AMP PEAK  9(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            88                            342 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            88                            342 
[1] "AMP PEAK 10(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                            107                             323 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                            107                             323 
[1] "AMP PEAK 11(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                            261                             169 
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                            261                             169 
[1] "AMP PEAK 12(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                           265                            165 
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                           265                            165 
[1] "AMP PEAK 13(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                           120                            310 
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                           120                            310 
[1] "AMP PEAK 14(16Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                           106                            324 
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                           106                            324 
[1] "AMP PEAK 15(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                            42                            388 
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                            42                            388 
[1] "AMP PEAK 16(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                         107                          323 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                         107                          323 
[1] "AMP PEAK 17(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            99                            331 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            99                            331 
[1] "AMP PEAK 18(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                            70                            360 
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                            70                            360 
[1] "AMP PEAK 19(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                             89                             341 
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                             89                             341 
[1] "AMP PEAK 20(20P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                            211                             219 
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                            211                             219 
[1] "AMP PEAK 21(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            307                             123 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            307                             123 
[1] "AMP PEAK 22(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                         308                          122 
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                         308                          122 
[1] "AMP PEAK 23(20Q13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                            311                             119 
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                            311                             119 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           161                            269 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           161                            269 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        117                         313 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        117                         313 
[1] "DEL PEAK  3(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          112                           318 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          112                           318 
[1] "DEL PEAK  4(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         51                         379 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         51                         379 
[1] "DEL PEAK  5(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         414 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         414 
[1] "DEL PEAK  6(2Q32.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           14                           416 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           14                           416 
[1] "DEL PEAK  7(3P26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           66                           364 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           66                           364 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           81                           349 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           81                           349 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  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 
                            44                            386 
[1] "DEL PEAK 10(4P16.2) MUTATION ANALYSIS"
[1] 3
  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 
                          128                           302 
[1] "DEL PEAK 11(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          138                           292 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          138                           292 
[1] "DEL PEAK 12(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          146                           284 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          146                           284 
[1] "DEL PEAK 13(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           96                           334 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           96                           334 
[1] "DEL PEAK 14(5Q21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                          121                           309 
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                          121                           309 
[1] "DEL PEAK 15(5Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                          112                           318 
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                          112                           318 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           376 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           376 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         60                         370 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         60                         370 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           418 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           418 
[1] "DEL PEAK 19(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          178                           252 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          178                           252 
[1] "DEL PEAK 20(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        192                         238 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        192                         238 
[1] "DEL PEAK 21(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                            45                            385 
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                            45                            385 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           371 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           371 
[1] "DEL PEAK 23(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            75                            355 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            75                            355 
[1] "DEL PEAK 24(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            90                            340 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            90                            340 
[1] "DEL PEAK 25(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            102                             328 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            102                             328 
[1] "DEL PEAK 26(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           103                            327 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           103                            327 
[1] "DEL PEAK 27(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            54                            376 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            54                            376 
[1] "DEL PEAK 28(13Q14.13) MUTATION ANALYSIS"
[1] 3
  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 
                             18                             412 
[1] "DEL PEAK 29(14Q31.1) MUTATION ANALYSIS"
[1] 3
  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 
                           141                            289 
[1] "DEL PEAK 30(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           166                            264 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           166                            264 
[1] "DEL PEAK 31(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           160                            270 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           160                            270 
[1] "DEL PEAK 32(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           158                            272 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           158                            272 
[1] "DEL PEAK 33(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            152                             278 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            152                             278 
[1] "DEL PEAK 34(16P13.3) MUTATION ANALYSIS"
[1] 3
  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 
                            52                            378 
[1] "DEL PEAK 35(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            56                            374 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            56                            374 
[1] "DEL PEAK 36(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         239                          191 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         239                          191 
[1] "DEL PEAK 37(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            64                            366 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            64                            366 
[1] "DEL PEAK 38(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            231                             199 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            231                             199 
[1] "DEL PEAK 39(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           257                            173 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           257                            173 
[1] "DEL PEAK 40(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           271                            159 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           271                            159 
[1] "DEL PEAK 41(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                           271                            159 
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                           271                            159 
[1] "DEL PEAK 42(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                            59                            371 
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                            59                            371 
[1] "DEL PEAK 43(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                           121                            309 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                           121                            309 
[1] "DEL PEAK 44(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           121                            309 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           121                            309 
[1] "DEL PEAK 45(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           135                            295 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           135                            295 
[1] "DEL PEAK 46(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            150                             280 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            150                             280 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 430 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
         154         1126         1419         1331         1321          711 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
         541         1286         1366         1068         1387           NA 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
         472         1127         1133          488         1054         1111 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
          NA          987         1001          962          926          888 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
        1020          718          672          671          995          887 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
         824          685          734          255          763          766 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
         735          627          662          751          742          726 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
         612          598          617           NA           NA           NA 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
        1595          293           NA           31           NA           31 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1127           31         1065         1765         1946          212 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
          31           NA         1186           31          276          731 
TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 
          NA         1127         1096          245          580           NA 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
          NA          580         1035          882          882          791 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
         395           30          426         1034          639           NA 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
         730          546          911          700          638          608 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
         424          608         1856         2375          184          212 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        1643           NA          426           28         1522         1431 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 
        1430          457           NA          182           NA         1127 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 
         578           NA           NA           NA           NA         2587 
TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
         821           NA          579           30           30         1066 
TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
          NA           NA          761           31          547          485 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
        1186         1124         1126          454           NA          518 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
          30           NA         1006           NA         1096          975 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
          30          945          945         1612          518          731 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA          912           NA          549          943           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
         395          730         1004          791          730           NA 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
         638         1035           61          669          489         1551 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
         397         1036          791          761          730          822 
TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
          NA          580           NA          822          424         1157 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
         578          913         1035          549          549          518 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
          NA          822         1278           30          518          456 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
         669         1064          457          457           30          974 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
         365          943          943           NA           31         1065 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 
          31         1005         1065          791         1126           NA 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
          NA         1581           NA         1216           NA           NA 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
          28           NA         1247         1216           NA         1246 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
           2          650          128         1720           24           22 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ 
          48           31            3           23            6           NA 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
          13           14           28          441          824           NA 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
          NA          479            6          652          542          158 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
         168         2289         1532         1776           NA           NA 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1002           NA         2549           NA         1977           NA 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
        1868           NA           NA           NA           NA           NA 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
          NA           NA           NA           NA           68           93 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
          65           99          100            2            8           10 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
           3           41          534         3116         1227         2134 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 
         475         1466         1561          669           NA           NA 
TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
          NA           89           61         3780          701          609 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
        1126          244          792          244          822          396 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
         884          670          699          915          487          457 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
          NA          457          457          518          457          365 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
         427          883          488          669          456          395 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
         396          457          427          335          394          397 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
         337          337          335          306          366          456 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
         373          596          411          350          614          621 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
         540          555           40          241          460          543 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
         137          521          380          491          474          229 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
         377          308          378          435          275          287 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
         354          408           46          365          346          312 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
        3641          743         1162         3974         2821         1518 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
         405          383         4270          228         1348         4000 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        4126          236         4233          186          427          805 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        2475         3648         1094         1849         3561         2988 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
        2895           NA          407           NA          415          409 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
          NA         1091           47          496          900          494 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
        1024           39           16         1077          591         3275 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
          NA          254         2506           NA         2268         1310 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
        1882         1631         1359         1674         1574         1372 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
        1199         1093         1117         1095          804          672 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
         792          419         1089          796         2792           NA 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
        1434         1606          125          154           85          182 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
         170          821          526          449 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=77,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=273,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
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.
Variable 21:'BATCH.NUMBER':	nDistinctValues=20,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [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"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 430 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  10  76 294  48 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   11    76   294    48 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  10  76 294  48 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   11    76   294    48 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
252 101  76 
[1] "table(vv)"
vv
 N0  N1  N2 
252 101  76 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
252 101  76 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
252 101  76 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
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    59  19
  AMP PEAK  1(2Q33.1) WILD-TYPE 270  65
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           78                           335 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           19                            65 
$`AMP PEAK  1(2Q33.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
        5.06        37.02        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       30.44        32.71        29.16        24.16        24.69        23.87 
TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3562 
       24.92         1.02        34.03        29.00        29.00        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       50.04        15.02        37.05         5.03         0.99        35.05 
TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3979 TCGA-AA-A00W TCGA-AA-A01I 
       33.07        24.03        16.08        24.00        14.99        31.00 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        1.02        26.01         2.96        21.37         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
        1.02         0.10         0.20         0.43        16.31         0.20 
TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
        5.13         3.19         0.07         0.26        40.34        21.99 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        8.02        29.06         5.03        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 
       29.03        21.99        14.99        14.99        11.51         4.50 
TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 
       17.13         7.53        24.43         7.50         7.76        14.04 
TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6299 
       26.47        35.97         8.61         1.55         8.35        74.56 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-QG-A5YX 
       45.11        39.42        47.15        52.80         4.11        17.29 

$`AMP PEAK  1(2Q33.1) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.25        16.04        32.45        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        19.07        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-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-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
        0.92        47.05        47.01        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 
       36.00        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       12.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       40.96         0.07        56.55         0.79         0.72         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         5.52        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-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        48.20 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.01         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-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         7.92 
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         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6314 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-A50V 
       13.78        35.80        26.17        91.79        46.75         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        14.76 

  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                         0.07                          0.07 
  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 
                        17.08                         20.19 
[1] "0.1 - 74.6 (17.1)"  "0.1 - 140.4 (20.2)"
[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        17         0
  AMP PEAK  1(2Q33.1) WILD-TYPE      59        1       23       110         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(2Q33.1) MUTATED           1         5          4         13
  AMP PEAK  1(2Q33.1) WILD-TYPE         0        16          9         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(2Q33.1) MUTATED           11        9         3         0
  AMP PEAK  1(2Q33.1) WILD-TYPE         27       33        13         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  STAGE I                             13                            59
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           17                           110
  STAGE IIB                            0                             8
  STAGE IIC                            1                             0
  STAGE III                            5                            16
  STAGE IIIA                           4                             9
  STAGE IIIB                          13                            40
  STAGE IIIC                          11                            27
  STAGE IV                             9                            33
  STAGE IVA                            3                            13
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  1(2Q33.1) MUTATED       3  14  59   8
  AMP PEAK  1(2Q33.1) WILD-TYPE     8  62 235  40
D1V4, multiclass
       clus
vv      AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  T0+T1                           3                             8
  T2                             14                            62
  T3                             59                           235
  T4                              8                            40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  1(2Q33.1) MUTATED    40  21  22
  AMP PEAK  1(2Q33.1) WILD-TYPE 212  80  54
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  N0                          40                           212
  N1                          21                            80
  N2                          22                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  1(2Q33.1) MUTATED    57  10   2   0  14
  AMP PEAK  1(2Q33.1) WILD-TYPE 263  40   5   1  31
D1V6, multiclass
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  M0                           57                           263
  M1                           10                            40
  M1A                           2                             5
  M1B                           0                             1
  MX                           14                            31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    36  48
  AMP PEAK  1(2Q33.1) WILD-TYPE 167 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     36   48
  AMP PEAK  1(2Q33.1) WILD-TYPE  167  179
        clus
vv       AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  FEMALE                          36                           167
  MALE                            48                           179
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    76   8
  AMP PEAK  1(2Q33.1) WILD-TYPE 297  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     76    8
  AMP PEAK  1(2Q33.1) WILD-TYPE  297   47
                               clus
vv                              AMP PEAK  1(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                   76
  COLON MUCINOUS ADENOCARCINOMA                           8
                               clus
vv                              AMP PEAK  1(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    297
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED     1  83
  AMP PEAK  1(2Q33.1) WILD-TYPE   2 344
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED      1   83
  AMP PEAK  1(2Q33.1) WILD-TYPE    2  344
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  NO                            1                             2
  YES                          83                           344
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(2Q33.1) MUTATED    51   2   6   6
  AMP PEAK  1(2Q33.1) WILD-TYPE 254   1  18  18
D1V10, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  R0                          51                           254
  R1                           2                             1
  R2                           6                            18
  RX                           6                            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"
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                           9    47
  AMP PEAK  1(2Q33.1) WILD-TYPE                        32   164
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     47
                                  clus
vv                                 AMP PEAK  1(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   32
  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    63  17
  AMP PEAK  2(5P13.2) WILD-TYPE 266  67
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           80                           333 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           17                            67 
$`AMP PEAK  2(5P13.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 
        5.06        43.76        43.43        44.91        45.60        37.25 
TCGA-A6-3807 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         0.99        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         0.99 
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         1.58 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 
        0.43         0.92         0.20        62.79        49.41        29.56 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 
        1.94         2.24        48.20         8.02        13.02        16.01 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 
       15.02        14.04        29.03        14.99        13.02        11.01 
TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6924 TCGA-D5-6929 
       19.59        17.75        17.13         7.53        14.30        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28K 
       12.00        11.38        12.59         7.50         6.12        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6625 
       95.18        13.38         1.55        35.41        82.39        91.79 
TCGA-G4-6626 TCGA-G4-6627 
       46.75        47.15 

$`AMP PEAK  2(5P13.2) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       37.02        46.65        23.38        17.79        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       13.94        15.52        37.05        16.04        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 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-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        52.44         9.63         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       61.02        78.08         6.05         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 
        0.92        50.04        47.05        15.02        11.01        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 
       36.95        17.03         0.99        33.07        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 
       17.03         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         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         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         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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-5407 
       32.94         5.13        83.80        22.36        65.00        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10       100.01         5.23        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.01         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-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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
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-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04         9.44        11.64         1.51        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-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-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
      117.07         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         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
        0.53        19.43       107.67        28.21         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                         0.20                          0.07 
  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 
                       18.375                        20.190 
[1] "0.2 - 98.2 (18.4)"  "0.1 - 140.4 (20.2)"
[1] "hr=" "1.1"
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      58        1       23       105         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(5P13.2) MUTATED           0         3          4          4
  AMP PEAK  2(5P13.2) WILD-TYPE         1        18          9         49
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(5P13.2) MUTATED           13       12         2         0
  AMP PEAK  2(5P13.2) WILD-TYPE         25       30        14         1
D2V3, multiclass
            clus
vv           AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  STAGE I                             14                            58
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           22                           105
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           4                             9
  STAGE IIIB                           4                            49
  STAGE IIIC                          13                            25
  STAGE IV                            12                            30
  STAGE IVA                            2                            14
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  2(5P13.2) MUTATED       1  18  57   6
  AMP PEAK  2(5P13.2) WILD-TYPE    10  58 237  42
D2V4, multiclass
       clus
vv      AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  T0+T1                           1                            10
  T2                             18                            58
  T3                             57                           237
  T4                              6                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  2(5P13.2) MUTATED    42  18  22
  AMP PEAK  2(5P13.2) WILD-TYPE 210  83  54
D2V5, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  N0                          42                           210
  N1                          18                            83
  N2                          22                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  2(5P13.2) MUTATED    56  12   2   0   9
  AMP PEAK  2(5P13.2) WILD-TYPE 264  38   5   1  36
D2V6, multiclass
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  M0                           56                           264
  M1                           12                            38
  M1A                           2                             5
  M1B                           0                             1
  MX                            9                            36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    43  39
  AMP PEAK  2(5P13.2) WILD-TYPE 160 188
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     43   39
  AMP PEAK  2(5P13.2) WILD-TYPE  160  188
        clus
vv       AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  FEMALE                          43                           160
  MALE                            39                           188
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    71  11
  AMP PEAK  2(5P13.2) WILD-TYPE 302  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     71   11
  AMP PEAK  2(5P13.2) WILD-TYPE  302   44
                               clus
vv                              AMP PEAK  2(5P13.2) MUTATED
  COLON ADENOCARCINOMA                                   71
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              AMP PEAK  2(5P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    302
  COLON MUCINOUS ADENOCARCINOMA                            44
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED     0  82
  AMP PEAK  2(5P13.2) WILD-TYPE   3 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED      0   82
  AMP PEAK  2(5P13.2) WILD-TYPE    3  345
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  NO                            0                             3
  YES                          82                           345
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(5P13.2) MUTATED    59   0   8   2
  AMP PEAK  2(5P13.2) WILD-TYPE 246   3  16  22
D2V10, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  R0                          59                           246
  R1                           0                             3
  R2                           8                            16
  RX                           2                            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"
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                           7    41
  AMP PEAK  2(5P13.2) WILD-TYPE                        34   170
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(5P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     41
                                  clus
vv                                 AMP PEAK  2(5P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   34
  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    35   7
  AMP PEAK  3(5Q22.3) WILD-TYPE 294  77
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           42                           371 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                            7                            77 
$`AMP PEAK  3(5Q22.3) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
        5.06        44.91        45.60        37.25        34.65        32.45 
TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3715 
       25.08        20.61         5.03        15.02         5.98         0.99 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       14.93        24.03        12.99        13.05        34.06        26.01 
TCGA-AA-3994 TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-4684 
       27.02        40.96         1.58         0.43        15.75        65.00 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 
       49.41        11.74        16.01         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6932 TCGA-DM-A1D0 
       14.99        11.01        17.75         1.32        11.38       130.65 
TCGA-DM-A1D8 TCGA-DM-A28M TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6627 TCGA-NH-A6GB 
       12.59        95.18        13.38        44.68        47.15         5.59 

$`AMP PEAK  3(5Q22.3) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 
       42.28        35.11        13.94        15.52        37.05        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 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-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-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-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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       37.02        17.03         0.99        33.07        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        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-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         1.02         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.20        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       17.03        12.00        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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-F4-6703 
        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         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6307 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-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        46.75        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98        26.99        17.29        14.76 

  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         0.43                          0.07 
  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 
                       15.385                        20.190 
[1] "0.4 - 130.7 (15.4)" "0.1 - 140.4 (20.2)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5Q22.3) MUTATED         6        0        2        11         1
  AMP PEAK  3(5Q22.3) WILD-TYPE      66        1       26       116         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         12         49
                               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         33       36        11         1
D3V3, multiclass
            clus
vv           AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  STAGE I                              6                            66
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           11                           116
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            12
  STAGE IIIB                           4                            49
  STAGE IIIC                           5                            33
  STAGE IV                             6                            36
  STAGE IVA                            5                            11
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  3(5Q22.3) MUTATED       1   7  29   6
  AMP PEAK  3(5Q22.3) WILD-TYPE    10  69 265  42
D3V4, multiclass
       clus
vv      AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  T0+T1                           1                            10
  T2                              7                            69
  T3                             29                           265
  T4                              6                            42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  3(5Q22.3) MUTATED    21  11  11
  AMP PEAK  3(5Q22.3) WILD-TYPE 231  90  65
D3V5, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  N0                          21                           231
  N1                          11                            90
  N2                          11                            65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  3(5Q22.3) MUTATED    26   8   3   0   4
  AMP PEAK  3(5Q22.3) WILD-TYPE 294  42   4   1  41
D3V6, multiclass
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  M0                           26                           294
  M1                            8                            42
  M1A                           3                             4
  M1B                           0                             1
  MX                            4                            41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    22  21
  AMP PEAK  3(5Q22.3) WILD-TYPE 181 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     22   21
  AMP PEAK  3(5Q22.3) WILD-TYPE  181  206
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  FEMALE                          22                           181
  MALE                            21                           206
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    40   3
  AMP PEAK  3(5Q22.3) WILD-TYPE 333  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     40    3
  AMP PEAK  3(5Q22.3) WILD-TYPE  333   52
                               clus
vv                              AMP PEAK  3(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                   40
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              AMP PEAK  3(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    333
  COLON MUCINOUS ADENOCARCINOMA                            52
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED     1  42
  AMP PEAK  3(5Q22.3) WILD-TYPE   2 385
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      1   42
  AMP PEAK  3(5Q22.3) WILD-TYPE    2  385
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  NO                            1                             2
  YES                          42                           385
[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 276   3  19  24
D3V10, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  R0                          29                           276
  R1                           0                             3
  R2                           5                            19
  RX                           0                            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"
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                           7    23
  AMP PEAK  3(5Q22.3) WILD-TYPE                        34   188
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     23
                                  clus
vv                                 AMP PEAK  3(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   34
  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    70  17
  AMP PEAK  4(6P21.1) WILD-TYPE 259  67
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           87                           326 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           17                            67 
$`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        52.44 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3561 
       29.00        29.00        12.99        13.02        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3846 
       19.99        15.02        85.05         0.99        35.05        17.03 
TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 
        0.99        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         1.02         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         5.19        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 
       39.42        91.79        46.75 

$`AMP PEAK  4(6P21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.76        23.38        17.79 
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        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        34.65        14.53        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        24.13         8.38        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-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       36.95        37.02        14.93        33.07        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 
       17.03         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         0.99        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         1.58         0.10         0.76         0.43 
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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94         5.13        83.80        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        48.20        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5861 
       37.02         8.02        26.04        27.02        22.03        15.02 
TCGA-CM-5863 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-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        14.99        12.26        13.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       17.75        18.25         7.92        17.85         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-F4-6461 TCGA-F4-6463 
       81.37       119.93        35.97        60.79        11.11        13.64 
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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6298 
        1.28        35.41        19.43       107.67         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
        4.11         5.06         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                         0.20                          0.07 
  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 
                       17.130                        20.155 
[1] "0.2 - 117.1 (17.1)" "0.1 - 140.4 (20.2)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(6P21.1) MUTATED        12        0        1        24         1
  AMP PEAK  4(6P21.1) WILD-TYPE      60        1       27       103         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(6P21.1) MUTATED           0         4          6         14
  AMP PEAK  4(6P21.1) WILD-TYPE         1        17          7         39
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(6P21.1) MUTATED           12       10         5         0
  AMP PEAK  4(6P21.1) WILD-TYPE         26       32        11         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  STAGE I                             12                            60
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           24                           103
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             7
  STAGE IIIB                          14                            39
  STAGE IIIC                          12                            26
  STAGE IV                            10                            32
  STAGE IVA                            5                            11
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  4(6P21.1) MUTATED       2  13  69   7
  AMP PEAK  4(6P21.1) WILD-TYPE     9  63 225  41
D4V4, multiclass
       clus
vv      AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  T0+T1                           2                             9
  T2                             13                            63
  T3                             69                           225
  T4                              7                            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  4(6P21.1) MUTATED    44  21  26
  AMP PEAK  4(6P21.1) WILD-TYPE 208  80  50
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          44                           208
  N1                          21                            80
  N2                          26                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  4(6P21.1) MUTATED    66  12   3   0   7
  AMP PEAK  4(6P21.1) WILD-TYPE 254  38   4   1  38
D4V6, multiclass
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  M0                           66                           254
  M1                           12                            38
  M1A                           3                             4
  M1B                           0                             1
  MX                            7                            38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    38  53
  AMP PEAK  4(6P21.1) WILD-TYPE 165 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     38   53
  AMP PEAK  4(6P21.1) WILD-TYPE  165  174
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          38                           165
  MALE                            53                           174
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    84   6
  AMP PEAK  4(6P21.1) WILD-TYPE 289  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     84    6
  AMP PEAK  4(6P21.1) WILD-TYPE  289   49
                               clus
vv                              AMP PEAK  4(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                   84
  COLON MUCINOUS ADENOCARCINOMA                           6
                               clus
vv                              AMP PEAK  4(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    289
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED     3  88
  AMP PEAK  4(6P21.1) WILD-TYPE   0 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED      3   88
  AMP PEAK  4(6P21.1) WILD-TYPE    0  339
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                            3                             0
  YES                          88                           339
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(6P21.1) MUTATED    64   0   7   4
  AMP PEAK  4(6P21.1) WILD-TYPE 241   3  17  20
D4V10, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                          64                           241
  R1                           0                             3
  R2                           7                            17
  RX                           4                            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"
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                           6    53
  AMP PEAK  4(6P21.1) WILD-TYPE                        35   158
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     53
                                  clus
vv                                 AMP PEAK  4(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   35
  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(8P11.23) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(8P11.23) MUTATED   115  26
  AMP PEAK  5(8P11.23) WILD-TYPE 214  58
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                           141                            272 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            26                             58 
$`AMP PEAK  5(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 
        5.06        43.43        17.79        45.60        13.94        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6648 
       32.45        32.91        32.71        29.16        27.09        25.18 
TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.16        20.28         9.63        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 
        6.97         1.02        36.03        19.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       12.99        33.99        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-3681 
        6.97        54.02        14.01        50.04        47.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       37.05        19.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3875 
       36.95        17.03        31.07        31.07        24.03        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00K TCGA-AA-A00R 
       12.99        24.00        34.06        24.00        18.05         0.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
       21.99         0.99         1.02        37.02        51.98         0.92 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-4070 
        0.07         1.58         0.10         0.43        27.09        16.31 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44         5.19         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-AZ-6608 
       22.36        62.79        61.41        49.41         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 
        2.24         3.06         2.14         3.29         0.07       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       15.62        48.20        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
        8.02         8.02        22.98        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        29.03        21.99        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-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       11.51        20.19         1.32         4.50        17.13        16.14 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 
        7.53        12.43        14.30         9.04        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H 
      119.70        38.20         7.50        44.32         6.12       117.07 
TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 
       98.24        13.45         6.18        16.24        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       53.62        45.11        39.42        26.43        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX 
        4.11         5.59        17.29 

$`AMP PEAK  5(8P11.23) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       35.11        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       19.66        16.24        24.92        61.84        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        1.02         3.02         1.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       13.94        61.02         2.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        36.00        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       39.06         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         1.02         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        14.50         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       11.74         3.25         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        40.34        70.16        21.99        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       22.03        30.08        17.03        12.00        14.04        16.04 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        19.59        13.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
       18.25         7.92        15.12        17.85        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39        10.13         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       95.18         8.61        13.38        11.11        13.64        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        91.79        52.80         5.06         2.79         5.98 
TCGA-QG-A5YV TCGA-QG-A5Z2 
       26.99        14.76 

  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                        119.70                         140.38 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                        17.290                         21.565 
[1] "0.1 - 119.7 (17.3)" "0.1 - 140.4 (21.6)"
[1] "hr=" "1"  
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(8P11.23) MUTATED        31        0       15        37         3
  AMP PEAK  5(8P11.23) WILD-TYPE      41        1       13        90         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(8P11.23) MUTATED           1         8          4         16
  AMP PEAK  5(8P11.23) WILD-TYPE         0        13          9         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(8P11.23) MUTATED           15       14         6         0
  AMP PEAK  5(8P11.23) WILD-TYPE         23       28        10         1
D5V3, multiclass
            clus
vv           AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  STAGE I                              31                             41
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            37                             90
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            4                              9
  STAGE IIIB                           16                             37
  STAGE IIIC                           15                             23
  STAGE IV                             14                             28
  STAGE IVA                             6                             10
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  5(8P11.23) MUTATED       3  31 100  17
  AMP PEAK  5(8P11.23) WILD-TYPE     8  45 194  31
D5V4, multiclass
       clus
vv      AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  T0+T1                            3                              8
  T2                              31                             45
  T3                             100                            194
  T4                              17                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  5(8P11.23) MUTATED    92  32  27
  AMP PEAK  5(8P11.23) WILD-TYPE 160  69  49
D5V5, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  N0                           92                            160
  N1                           32                             69
  N2                           27                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  5(8P11.23) MUTATED   111  16   4   0  19
  AMP PEAK  5(8P11.23) WILD-TYPE 209  34   3   1  26
D5V6, multiclass
     clus
vv    AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  M0                           111                            209
  M1                            16                             34
  M1A                            4                              3
  M1B                            0                              1
  MX                            19                             26
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.23) MUTATED    73  78
  AMP PEAK  5(8P11.23) WILD-TYPE 130 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     73   78
  AMP PEAK  5(8P11.23) WILD-TYPE  130  149
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  FEMALE                           73                            130
  MALE                             78                            149
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.23) MUTATED   137  14
  AMP PEAK  5(8P11.23) WILD-TYPE 236  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED    137   14
  AMP PEAK  5(8P11.23) WILD-TYPE  236   41
                               clus
vv                              AMP PEAK  5(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                   137
  COLON MUCINOUS ADENOCARCINOMA                           14
                               clus
vv                              AMP PEAK  5(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                     236
  COLON MUCINOUS ADENOCARCINOMA                             41
[1] 2 2
[1] FALSE
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.23) MUTATED     2 149
  AMP PEAK  5(8P11.23) WILD-TYPE   1 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED      2  149
  AMP PEAK  5(8P11.23) WILD-TYPE    1  278
     clus
vv    AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  NO                             2                              1
  YES                          149                            278
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(8P11.23) MUTATED   109   1   9  11
  AMP PEAK  5(8P11.23) WILD-TYPE 196   2  15  13
D5V10, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  R0                          109                            196
  R1                            1                              2
  R2                            9                             15
  RX                           11                             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"
D5V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(8P11.23) MUTATED                                  0     5
  AMP PEAK  5(8P11.23) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(8P11.23) MUTATED                          12    81
  AMP PEAK  5(8P11.23) WILD-TYPE                        29   130
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      81
                                  clus
vv                                 AMP PEAK  5(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    29
  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(6) Variable = AMP PEAK  6(8P11.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8P11.21) MUTATED   139  31
  AMP PEAK  6(8P11.21) WILD-TYPE 190  53
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                           170                            243 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            31                             53 
$`AMP PEAK  6(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5666 
       45.60        13.94        34.65        32.45        31.63        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       29.16        27.09        25.08        25.18        24.16        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       61.84         9.63         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
        6.97         1.02        36.03        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        19.99        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       36.95        17.03        31.07        24.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 
        2.01        12.99        24.00        16.08        34.06        24.00 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01G 
       19.00        18.05         0.99        17.03        21.99        12.00 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
        1.02        37.02        51.98         0.92        41.00         0.07 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 
        4.21         1.58         1.02         0.10         0.43         0.92 
TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       27.09        21.44         5.19        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36        62.79        61.41        49.41         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        0.07         1.35       102.44        15.62        48.20        51.32 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
        2.01        20.02        37.02         8.02         8.02        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        29.03        14.99        12.99        13.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 
       11.01        11.08        11.08        10.06        11.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
        1.32         7.92         4.50        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA 
       11.38        10.26       119.70        38.20       130.65         7.50 
TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
       44.32         6.12        98.24         8.61        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 
        6.18        16.31        16.24         8.35        43.07        53.62 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       44.68        45.11        39.42        26.43        46.75        47.15 
TCGA-NH-A50T TCGA-QG-A5YX 
        4.11        17.29 

$`AMP PEAK  6(8P11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        42.28        44.91        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       37.25        16.04        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       29.19        33.53        23.61        22.09        22.06        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        5.03         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3672 
       23.01        13.94        61.02         6.05         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       47.05        11.01        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 
       31.07        53.00        17.03        29.98        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       21.99        50.99        13.05        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       31.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        5.03        22.03        39.98        18.05        40.96        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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        21.01         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        14.99        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         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        61.87        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         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5Z2 
        5.59        26.99        14.76 

  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                         17.03                          22.03 
[1] "0.1 - 130.7 (17.0)" "0.1 - 140.4 (22.0)"
[1] "hr=" "1"  
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(8P11.21) MUTATED        33        0       17        48         3
  AMP PEAK  6(8P11.21) WILD-TYPE      39        1       11        79         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8P11.21) MUTATED           1         9          5         21
  AMP PEAK  6(8P11.21) WILD-TYPE         0        12          8         32
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8P11.21) MUTATED           12       22         6         0
  AMP PEAK  6(8P11.21) WILD-TYPE         26       20        10         1
D6V3, multiclass
            clus
vv           AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  STAGE I                              33                             39
  STAGE IA                              0                              1
  STAGE II                             17                             11
  STAGE IIA                            48                             79
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             9                             12
  STAGE IIIA                            5                              8
  STAGE IIIB                           21                             32
  STAGE IIIC                           12                             26
  STAGE IV                             22                             20
  STAGE IVA                             6                             10
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  6(8P11.21) MUTATED       3  35 123  18
  AMP PEAK  6(8P11.21) WILD-TYPE     8  41 171  30
D6V4, multiclass
       clus
vv      AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  T0+T1                            3                              8
  T2                              35                             41
  T3                             123                            171
  T4                              18                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  6(8P11.21) MUTATED   109  38  31
  AMP PEAK  6(8P11.21) WILD-TYPE 143  63  45
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  N0                          109                            143
  N1                           38                             63
  N2                           31                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  6(8P11.21) MUTATED   131  23   5   0  19
  AMP PEAK  6(8P11.21) WILD-TYPE 189  27   2   1  26
D6V6, multiclass
     clus
vv    AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  M0                           131                            189
  M1                            23                             27
  M1A                            5                              2
  M1B                            0                              1
  MX                            19                             26
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.21) MUTATED    78 101
  AMP PEAK  6(8P11.21) WILD-TYPE 125 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     78  101
  AMP PEAK  6(8P11.21) WILD-TYPE  125  126
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  FEMALE                           78                            125
  MALE                            101                            126
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.21) MUTATED   161  18
  AMP PEAK  6(8P11.21) WILD-TYPE 212  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED    161   18
  AMP PEAK  6(8P11.21) WILD-TYPE  212   37
                               clus
vv                              AMP PEAK  6(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                   161
  COLON MUCINOUS ADENOCARCINOMA                           18
                               clus
vv                              AMP PEAK  6(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     212
  COLON MUCINOUS ADENOCARCINOMA                             37
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.21) MUTATED     2 177
  AMP PEAK  6(8P11.21) WILD-TYPE   1 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED      2  177
  AMP PEAK  6(8P11.21) WILD-TYPE    1  250
     clus
vv    AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  NO                             2                              1
  YES                          177                            250
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8P11.21) MUTATED   128   0  13  12
  AMP PEAK  6(8P11.21) WILD-TYPE 177   3  11  12
D6V10, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  R0                          128                            177
  R1                            0                              3
  R2                           13                             11
  RX                           12                             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"
D6V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(8P11.21) MUTATED                                  0     6
  AMP PEAK  6(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8P11.21) MUTATED                          13    96
  AMP PEAK  6(8P11.21) WILD-TYPE                        28   115
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK  6(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    28
  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(7) Variable = AMP PEAK  7(8Q12.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(8Q12.1) MUTATED   173  40
  AMP PEAK  7(8Q12.1) WILD-TYPE 156  44
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                          213                           200 
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                           40                            44 
$`AMP PEAK  7(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 
        5.06        43.76        43.43        17.79        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       13.94        37.25        16.04        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       31.63        29.19        32.71        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        24.16        24.69        23.87        20.28 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         5.03         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
        6.97         1.02        36.03        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 
       36.00         5.03        19.04         0.99         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        17.03        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 
       24.00        34.03         2.01        16.08        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00L 
       24.00        27.02        13.94        19.00        18.05        17.03 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
        0.99        17.03        21.99        12.00        31.00         1.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
       51.98         2.96         5.03         0.92        41.00         0.07 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
        1.58         0.10         0.20         0.43         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4615 
       16.31         0.20        21.44         5.19        75.25        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 
        1.94         2.24         3.06         2.14         0.07         1.35 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      102.44        15.62        48.20        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        13.02        11.01        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 
       10.06        12.26        13.51        11.51        20.19         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
        7.92        15.12         4.50        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D9 
       11.38        10.26       119.70        38.20       130.65       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32         6.12        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       16.31        16.24         8.35        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       35.93        36.00        26.43        46.75        47.15         4.11 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX 
        5.98         5.59        17.29 

$`AMP PEAK  7(8Q12.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       37.02        46.65        23.38        42.28        44.91        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       37.05        34.65        14.53        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       22.09        22.06        22.52         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       24.39        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       52.44         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 
       23.01        19.99        13.94        61.02         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       47.05        11.01        19.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       14.93         0.99        36.03        32.05        31.07        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       31.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       21.99        50.99        13.05        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N 
       27.02        38.04        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        2.01        22.03        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         1.02         0.76 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        15.75        17.82         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-6599 TCGA-AZ-6601 
       50.37        58.39         1.41         5.65         6.77       100.01 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.25         3.29         0.26         0.33         0.10        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        21.01         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-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.01        12.03        14.99 
TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 
       19.59        20.42        17.75        18.25        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-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80         5.06         2.79 
TCGA-QG-A5YV TCGA-QG-A5Z2 
       26.99        14.76 

  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE 
                       17.130                        21.875 
[1] "0.1 - 140.4 (17.1)" "0.1 - 139.2 (21.9)"
[1] "hr=" "1.1"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(8Q12.1) MUTATED        37        0       16        62         3
  AMP PEAK  7(8Q12.1) WILD-TYPE      35        1       12        65         5
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8Q12.1) MUTATED           1         9          8         29
  AMP PEAK  7(8Q12.1) WILD-TYPE         0        12          5         24
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8Q12.1) MUTATED           20       27         9         0
  AMP PEAK  7(8Q12.1) WILD-TYPE         18       15         7         1
D7V3, multiclass
            clus
vv           AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  STAGE I                             37                            35
  STAGE IA                             0                             1
  STAGE II                            16                            12
  STAGE IIA                           62                            65
  STAGE IIB                            3                             5
  STAGE IIC                            1                             0
  STAGE III                            9                            12
  STAGE IIIA                           8                             5
  STAGE IIIB                          29                            24
  STAGE IIIC                          20                            18
  STAGE IV                            27                            15
  STAGE IVA                            9                             7
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  7(8Q12.1) MUTATED       4  41 155  24
  AMP PEAK  7(8Q12.1) WILD-TYPE     7  35 139  24
D7V4, multiclass
       clus
vv      AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  T0+T1                           4                             7
  T2                             41                            35
  T3                            155                           139
  T4                             24                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  7(8Q12.1) MUTATED   127  53  44
  AMP PEAK  7(8Q12.1) WILD-TYPE 125  48  32
D7V5, multiclass
    clus
vv   AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  N0                         127                           125
  N1                          53                            48
  N2                          44                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  7(8Q12.1) MUTATED   161  30   6   0  25
  AMP PEAK  7(8Q12.1) WILD-TYPE 159  20   1   1  20
D7V6, multiclass
     clus
vv    AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  M0                          161                           159
  M1                           30                            20
  M1A                           6                             1
  M1B                           0                             1
  MX                           25                            20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(8Q12.1) MUTATED   103 121
  AMP PEAK  7(8Q12.1) WILD-TYPE 100 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(8Q12.1) MUTATED    103  121
  AMP PEAK  7(8Q12.1) WILD-TYPE  100  106
        clus
vv       AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  FEMALE                         103                           100
  MALE                           121                           106
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(8Q12.1) MUTATED   204  20
  AMP PEAK  7(8Q12.1) WILD-TYPE 169  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(8Q12.1) MUTATED    204   20
  AMP PEAK  7(8Q12.1) WILD-TYPE  169   35
                               clus
vv                              AMP PEAK  7(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                  204
  COLON MUCINOUS ADENOCARCINOMA                          20
                               clus
vv                              AMP PEAK  7(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    169
  COLON MUCINOUS ADENOCARCINOMA                            35
[1] 2 2
[1] FALSE
D7V9, binary
                               cls
clus                              0   1
  AMP PEAK  7(8Q12.1) MUTATED     3 221
  AMP PEAK  7(8Q12.1) WILD-TYPE   0 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(8Q12.1) MUTATED      3  221
  AMP PEAK  7(8Q12.1) WILD-TYPE    0  206
     clus
vv    AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  NO                            3                             0
  YES                         221                           206
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(8Q12.1) MUTATED   155   1  16  13
  AMP PEAK  7(8Q12.1) WILD-TYPE 150   2   8  11
D7V10, multiclass
    clus
vv   AMP PEAK  7(8Q12.1) MUTATED AMP PEAK  7(8Q12.1) WILD-TYPE
  R0                         155                           150
  R1                           1                             2
  R2                          16                             8
  RX                          13                            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"
D7V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(8Q12.1) MUTATED                                  0     5
  AMP PEAK  7(8Q12.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q12.1) MUTATED                          21   119
  AMP PEAK  7(8Q12.1) WILD-TYPE                        20    92
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                    119
                                  clus
vv                                 AMP PEAK  7(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   20
  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(8) Variable = AMP PEAK  8(8Q24.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(8Q24.21) MUTATED   188  48
  AMP PEAK  8(8Q24.21) WILD-TYPE 141  36
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           236                            177 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                            48                             36 
$`AMP PEAK  8(8Q24.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       45.60        13.94        15.52        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        31.63        29.19        23.61 
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-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A56B 
       24.16        20.61        24.69        23.87        20.28        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         5.03         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 
        6.97         1.02        24.03        36.03        19.07        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-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       13.02        24.00        23.01        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       19.04         0.99         0.99        36.95        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       33.07        36.03         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03         2.01        16.08        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       24.00        27.02        13.94        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K 
       17.03        21.99        15.02         0.99        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
        1.02        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        0.92        41.00         0.07        21.37         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
        1.02         0.10         0.20         0.43         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4614 
       16.31         0.20        21.44         5.19        75.25         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-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.07         0.10         1.35       102.44        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       51.32        21.99         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       13.02        11.08        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19         1.32         7.92        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         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-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 
      119.70        24.43        38.20       130.65        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32         6.12        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       16.31        16.24         8.35        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       35.93        36.00        26.43        46.75        47.15         4.11 
TCGA-NH-A6GB TCGA-QG-A5YX 
        5.59        17.29 

$`AMP PEAK  8(8Q24.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-4105 
       46.65        23.38        42.28        44.91        37.05        14.53 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        22.52         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       61.84         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       38.99         1.02         9.07        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       34.03        21.01        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 
       61.02         2.01         0.92        47.05        11.01        19.00 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 
       15.95        38.99        14.93         0.99        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       53.00        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       21.99        50.99        13.05        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       27.02        38.04        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C 
        4.01        27.02        42.02        14.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       32.02        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y 
       35.01        26.01        39.06        39.98        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       18.05        40.96        56.55         0.79         0.72         0.76 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        15.75        17.82         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 
       50.37        58.39         1.41         6.77       100.01         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 
        0.26         0.33        17.56        40.34        70.16        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 
        2.93       124.27        23.05        26.04        22.03        12.00 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       16.04        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 
       11.08        11.01        12.03        14.99        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       18.25        17.85        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       12.00        92.75        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80         5.06         2.79 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 
        5.98        26.99        14.76 

  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                          0.07                           0.26 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                        18.525                         21.760 
[1] "0.1 - 140.4 (18.5)" "0.3 - 139.2 (21.8)"
[1] "hr=" "1.1"
D8V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8Q24.21) MUTATED        41        0       18        66         3
  AMP PEAK  8(8Q24.21) WILD-TYPE      31        1       10        61         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8Q24.21) MUTATED           1        10         10         32
  AMP PEAK  8(8Q24.21) WILD-TYPE         0        11          3         21
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8Q24.21) MUTATED           21       30        11         0
  AMP PEAK  8(8Q24.21) WILD-TYPE         17       12         5         1
D8V3, multiclass
            clus
vv           AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  STAGE I                              41                             31
  STAGE IA                              0                              1
  STAGE II                             18                             10
  STAGE IIA                            66                             61
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                            10                             11
  STAGE IIIA                           10                              3
  STAGE IIIB                           32                             21
  STAGE IIIC                           21                             17
  STAGE IV                             30                             12
  STAGE IVA                            11                              5
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  8(8Q24.21) MUTATED       4  47 171  25
  AMP PEAK  8(8Q24.21) WILD-TYPE     7  29 123  23
D8V4, multiclass
       clus
vv      AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  T0+T1                            4                              7
  T2                              47                             29
  T3                             171                            123
  T4                              25                             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  8(8Q24.21) MUTATED   141  56  49
  AMP PEAK  8(8Q24.21) WILD-TYPE 111  45  27
D8V5, multiclass
    clus
vv   AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  N0                          141                            111
  N1                           56                             45
  N2                           49                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  8(8Q24.21) MUTATED   178  35   6   0  26
  AMP PEAK  8(8Q24.21) WILD-TYPE 142  15   1   1  19
D8V6, multiclass
     clus
vv    AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  M0                           178                            142
  M1                            35                             15
  M1A                            6                              1
  M1B                            0                              1
  MX                            26                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   112 135
  AMP PEAK  8(8Q24.21) WILD-TYPE  91  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    112  135
  AMP PEAK  8(8Q24.21) WILD-TYPE   91   92
        clus
vv       AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  FEMALE                          112                             91
  MALE                            135                             92
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   221  25
  AMP PEAK  8(8Q24.21) WILD-TYPE 152  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    221   25
  AMP PEAK  8(8Q24.21) WILD-TYPE  152   30
                               clus
vv                              AMP PEAK  8(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                   221
  COLON MUCINOUS ADENOCARCINOMA                           25
                               clus
vv                              AMP PEAK  8(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     152
  COLON MUCINOUS ADENOCARCINOMA                             30
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED     3 244
  AMP PEAK  8(8Q24.21) WILD-TYPE   0 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED      3  244
  AMP PEAK  8(8Q24.21) WILD-TYPE    0  183
     clus
vv    AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  NO                             3                              0
  YES                          244                            183
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(8Q24.21) MUTATED   170   1  17  15
  AMP PEAK  8(8Q24.21) WILD-TYPE 135   2   7   9
D8V10, multiclass
    clus
vv   AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  R0                          170                            135
  R1                            1                              2
  R2                           17                              7
  RX                           15                              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"
D8V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(8Q24.21) MUTATED                                  0     7
  AMP PEAK  8(8Q24.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q24.21) MUTATED                          22   130
  AMP PEAK  8(8Q24.21) WILD-TYPE                        19    81
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK  8(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    19
  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(9) Variable = AMP PEAK  9(11P15.5) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(11P15.5) MUTATED    68  17
  AMP PEAK  9(11P15.5) WILD-TYPE 261  67
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            85                            328 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            17                             67 
$`AMP PEAK  9(11P15.5) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
       37.02        43.43        17.79        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3506 
       25.18        23.87         9.63         5.03         1.02        58.03 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3542 
        9.07        24.03        19.07        34.03        29.00        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 
       13.02        24.00        23.01        13.94        19.99        50.04 
TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3846 
       47.01         5.03        25.02        17.98        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 
       33.07         0.99        24.03        18.05        20.98        27.02 
TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S 
       19.07        34.03        17.03        21.99         0.99         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6888 TCGA-AD-6901 
       35.01        26.01        39.98         5.03         4.21         1.02 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
        0.46        16.31         0.95        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.19         1.94         2.14         0.07         0.26         1.35 
TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 
      102.44         8.02        30.08        17.03        29.03        21.99 
TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6898 
       11.08        12.26        13.51         1.32        17.85         7.53 
TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 
       13.41        49.91        35.97        60.79        13.38        13.64 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 
        8.35        74.56        61.87        55.04        45.11        35.93 
TCGA-QG-A5YV 
       26.99 

$`AMP PEAK  9(11P15.5) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
        5.06        46.65        43.76        23.38        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       29.16        27.09        22.52        24.13         8.38        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-A567 TCGA-A6-A56B TCGA-AA-3489 
       20.28        16.24        24.92        61.84        52.44         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02        37.05         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
        8.05        19.07        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       33.99        21.01        17.95        29.95        20.98        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 
        0.99         0.99        35.05         0.99         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       38.99        36.95        14.93         0.99        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        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-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-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
        0.99        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-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       33.04        37.02        39.06        51.98         2.96         2.01 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        56.55         0.79         0.72         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.43         0.92        14.50 
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         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-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        14.99 
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 
        7.92        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 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         1.28         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        43.07        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-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.98         5.59        17.29        14.76 

  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                        19.990                         20.005 
[1] "0.1 - 102.4 (20.0)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1"  
D9V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(11P15.5) MUTATED        11        0        4        21         1
  AMP PEAK  9(11P15.5) WILD-TYPE      61        1       24       106         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(11P15.5) MUTATED           0         4          4         13
  AMP PEAK  9(11P15.5) WILD-TYPE         1        17          9         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(11P15.5) MUTATED           11       12         5         0
  AMP PEAK  9(11P15.5) WILD-TYPE         27       30        11         1
D9V3, multiclass
            clus
vv           AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  STAGE I                              11                             61
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            21                            106
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            4                              9
  STAGE IIIB                           13                             40
  STAGE IIIC                           11                             27
  STAGE IV                             12                             30
  STAGE IVA                             5                             11
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  9(11P15.5) MUTATED       3  16  64   5
  AMP PEAK  9(11P15.5) WILD-TYPE     8  60 230  43
D9V4, multiclass
       clus
vv      AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  T0+T1                            3                              8
  T2                              16                             60
  T3                              64                            230
  T4                               5                             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  9(11P15.5) MUTATED    42  26  19
  AMP PEAK  9(11P15.5) WILD-TYPE 210  75  57
D9V5, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  N0                           42                            210
  N1                           26                             75
  N2                           19                             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  9(11P15.5) MUTATED    63  14   3   0   6
  AMP PEAK  9(11P15.5) WILD-TYPE 257  36   4   1  39
D9V6, multiclass
     clus
vv    AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  M0                            63                            257
  M1                            14                             36
  M1A                            3                              4
  M1B                            0                              1
  MX                             6                             39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED    44  44
  AMP PEAK  9(11P15.5) WILD-TYPE 159 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     44   44
  AMP PEAK  9(11P15.5) WILD-TYPE  159  183
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  FEMALE                           44                            159
  MALE                             44                            183
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED    83   3
  AMP PEAK  9(11P15.5) WILD-TYPE 290  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     83    3
  AMP PEAK  9(11P15.5) WILD-TYPE  290   52
                               clus
vv                              AMP PEAK  9(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                    83
  COLON MUCINOUS ADENOCARCINOMA                            3
                               clus
vv                              AMP PEAK  9(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                     290
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED     2  86
  AMP PEAK  9(11P15.5) WILD-TYPE   1 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED      2   86
  AMP PEAK  9(11P15.5) WILD-TYPE    1  341
     clus
vv    AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  NO                             2                              1
  YES                           86                            341
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(11P15.5) MUTATED    59   1   7   6
  AMP PEAK  9(11P15.5) WILD-TYPE 246   2  17  18
D9V10, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  R0                           59                            246
  R1                            1                              2
  R2                            7                             17
  RX                            6                             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"
D9V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(11P15.5) MUTATED                                  0     4
  AMP PEAK  9(11P15.5) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(11P15.5) MUTATED                           4    41
  AMP PEAK  9(11P15.5) WILD-TYPE                        37   170
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      41
                                  clus
vv                                 AMP PEAK  9(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    37
  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(10) Variable = AMP PEAK 10(12P13.33) MUTATION ANALYSIS
D10V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 10(12P13.33) MUTATED    76  22
  AMP PEAK 10(12P13.33) WILD-TYPE 253  62
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                             98                             315 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                             22                              62 
$`AMP PEAK 10(12P13.33) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
        5.06        44.91        13.94        16.04        34.65        14.53 
TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A566 
       22.09        25.08        20.61        20.12        20.28        24.92 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        58.03        36.03        29.00        29.00        12.99 
TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       19.99        78.08         0.92        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 
        5.03        26.99         0.99        35.05         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       14.93        33.07        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
        2.01        34.03        18.05        12.00        31.00        33.04 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       51.98         0.92        22.03        39.98        40.96         0.07 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 
        0.10         0.20         0.92         1.41         5.13        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CK-4948 
        6.77        11.74         3.19         1.94         3.06       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
       40.34        15.62        51.32         2.01        20.02         8.02 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 
       30.08        16.01        15.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 
       14.04        11.01        11.01        20.19        17.75         4.50 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       12.49        15.58        14.30        11.64        13.41        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A28M 
       10.26       119.70        24.43        13.32        44.32        95.18 
TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6323 
        8.61        35.87        16.31        44.68        35.93        13.78 
TCGA-G4-6627 TCGA-NH-A6GB 
       47.15         5.59 

$`AMP PEAK 10(12P13.33) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        23.61        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52        24.13         8.38        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 
       24.69        24.39        23.87        19.66        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       47.01        15.02        19.00        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       36.95        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 
       29.98        18.05        31.00         2.01        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
        1.02        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 
       39.98         2.01         5.03        41.00        18.05        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.43         0.46        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
      100.01        29.56         5.23         2.24         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        70.16        48.20        21.99        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       14.99        12.99        15.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.42        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       15.12        17.85        17.13        16.14         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 
       10.13        12.43         9.04         9.44         1.51        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        51.75        45.11        39.42        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        52.80         4.11         5.06         2.79         5.98 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                         16.025                          21.010 
[1] "0.1 - 119.7 (16.0)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.3"
D10V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(12P13.33) MUTATED        13        1        9        39         2
  AMP PEAK 10(12P13.33) WILD-TYPE      59        0       19        88         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(12P13.33) MUTATED           0         5          5          6
  AMP PEAK 10(12P13.33) WILD-TYPE         1        16          8         47
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(12P13.33) MUTATED           10       11         4         0
  AMP PEAK 10(12P13.33) WILD-TYPE         28       31        12         1
D10V3, multiclass
            clus
vv           AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  STAGE I                               13                              59
  STAGE IA                               1                               0
  STAGE II                               9                              19
  STAGE IIA                             39                              88
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             5                               8
  STAGE IIIB                             6                              47
  STAGE IIIC                            10                              28
  STAGE IV                              11                              31
  STAGE IVA                              4                              12
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 10(12P13.33) MUTATED       0  16  75  15
  AMP PEAK 10(12P13.33) WILD-TYPE    11  60 219  33
D10V4, multiclass
       clus
vv      AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  T0+T1                             0                              11
  T2                               16                              60
  T3                               75                             219
  T4                               15                              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 10(12P13.33) MUTATED    67  20  20
  AMP PEAK 10(12P13.33) WILD-TYPE 185  81  56
D10V5, multiclass
    clus
vv   AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  N0                            67                             185
  N1                            20                              81
  N2                            20                              56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 10(12P13.33) MUTATED    78  11   4   0  13
  AMP PEAK 10(12P13.33) WILD-TYPE 242  39   3   1  32
D10V6, multiclass
     clus
vv    AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  M0                             78                             242
  M1                             11                              39
  M1A                             4                               3
  M1B                             0                               1
  MX                             13                              32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                 cls
clus                                0   1
  AMP PEAK 10(12P13.33) MUTATED    52  55
  AMP PEAK 10(12P13.33) WILD-TYPE 151 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     52   55
  AMP PEAK 10(12P13.33) WILD-TYPE  151  172
        clus
vv       AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  FEMALE                            52                             151
  MALE                              55                             172
[1] 2 2
[1] FALSE
D10V8, binary
                                 cls
clus                                0   1
  AMP PEAK 10(12P13.33) MUTATED    95  12
  AMP PEAK 10(12P13.33) WILD-TYPE 278  43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     95   12
  AMP PEAK 10(12P13.33) WILD-TYPE  278   43
                               clus
vv                              AMP PEAK 10(12P13.33) MUTATED
  COLON ADENOCARCINOMA                                     95
  COLON MUCINOUS ADENOCARCINOMA                            12
                               clus
vv                              AMP PEAK 10(12P13.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      278
  COLON MUCINOUS ADENOCARCINOMA                              43
[1] 2 2
[1] FALSE
D10V9, binary
                                 cls
clus                                0   1
  AMP PEAK 10(12P13.33) MUTATED     0 107
  AMP PEAK 10(12P13.33) WILD-TYPE   3 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED      0  107
  AMP PEAK 10(12P13.33) WILD-TYPE    3  320
     clus
vv    AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  NO                              0                               3
  YES                           107                             320
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 10(12P13.33) MUTATED    78   1   3   5
  AMP PEAK 10(12P13.33) WILD-TYPE 227   2  21  19
D10V10, multiclass
    clus
vv   AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  R0                            78                             227
  R1                             1                               2
  R2                             3                              21
  RX                             5                              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(12P13.33) MUTATED                                  0     1
  AMP PEAK 10(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12P13.33) MUTATED                           8    55
  AMP PEAK 10(12P13.33) WILD-TYPE                        33   156
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       55
                                  clus
vv                                 AMP PEAK 10(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     33
  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(11) Variable = AMP PEAK 11(13Q12.13) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 11(13Q12.13) MUTATED   200  53
  AMP PEAK 11(13Q12.13) WILD-TYPE 129  31
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                            253                             160 
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                             53                              31 
$`AMP PEAK 11(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        5.06        37.02        46.65        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        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-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       19.99        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3841 
        0.99         0.99        35.05         0.99        25.02        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         0.99        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        12.99        24.00        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-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-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        17.03        42.02        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       15.02         0.99        32.02        12.00        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       21.37         0.79         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.43        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        5.19        75.25        50.37         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 
        5.23        11.74         1.94         2.24         3.06         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        1.35        17.56       102.44        48.20        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02         8.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        16.01         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       10.06        12.26        19.59        13.51        11.51        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       17.13        12.49         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        13.41        12.00        11.38        10.26       119.70 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32         7.50       131.51 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
        7.76         6.12        14.04        26.47       119.93        35.97 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        8.61        13.38         6.18        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 
       82.39        23.51        74.56        61.87        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-A6GB TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.59        26.99 
TCGA-QG-A5YX 
       17.29 

$`AMP PEAK 11(13Q12.13) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 
       19.07        17.95        29.95        23.01        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
       54.02         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       26.99        19.04         1.02        17.98        15.95        38.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
       33.07        36.03        53.00        18.05        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01         2.01        25.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       21.99        34.98        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 
        5.03         0.92        22.03        18.05         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72         0.76         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        0.20        17.82         5.52        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 
       61.41         6.77       100.01         3.19         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 
        3.29         0.26         0.33         0.10        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       37.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64         1.51        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
       98.24        95.18        11.11        13.64        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
        1.55        16.31        19.43        43.07        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 
       51.75        36.72        22.09        26.04        13.78        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       52.80         2.79         5.98        14.76 

  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE 
                         19.990                          20.155 
[1] "0.1 - 131.5 (20.0)" "0.1 - 140.4 (20.2)"
[1] "hr=" "1.1"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(13Q12.13) MUTATED        42        0       14        66         2
  AMP PEAK 11(13Q12.13) WILD-TYPE      30        1       14        61         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(13Q12.13) MUTATED           1        11         11         36
  AMP PEAK 11(13Q12.13) WILD-TYPE         0        10          2         17
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(13Q12.13) MUTATED           24       35        14         0
  AMP PEAK 11(13Q12.13) WILD-TYPE         14        7         2         1
D11V3, multiclass
            clus
vv           AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  STAGE I                               42                              30
  STAGE IA                               0                               1
  STAGE II                              14                              14
  STAGE IIA                             66                              61
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                             11                              10
  STAGE IIIA                            11                               2
  STAGE IIIB                            36                              17
  STAGE IIIC                            24                              14
  STAGE IV                              35                               7
  STAGE IVA                             14                               2
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 11(13Q12.13) MUTATED       7  45 181  28
  AMP PEAK 11(13Q12.13) WILD-TYPE     4  31 113  20
D11V4, multiclass
       clus
vv      AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  T0+T1                             7                               4
  T2                               45                              31
  T3                              181                             113
  T4                               28                              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 11(13Q12.13) MUTATED   135  74  52
  AMP PEAK 11(13Q12.13) WILD-TYPE 117  27  24
D11V5, multiclass
    clus
vv   AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  N0                           135                             117
  N1                            74                              27
  N2                            52                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 11(13Q12.13) MUTATED   185  41   7   0  25
  AMP PEAK 11(13Q12.13) WILD-TYPE 135   9   0   1  20
D11V6, multiclass
     clus
vv    AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  M0                            185                             135
  M1                             41                               9
  M1A                             7                               0
  M1B                             0                               1
  MX                             25                              20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                 cls
clus                                0   1
  AMP PEAK 11(13Q12.13) MUTATED   122 139
  AMP PEAK 11(13Q12.13) WILD-TYPE  81  88
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(13Q12.13) MUTATED    122  139
  AMP PEAK 11(13Q12.13) WILD-TYPE   81   88
        clus
vv       AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  FEMALE                           122                              81
  MALE                             139                              88
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(13Q12.13) MUTATED   244  16
  AMP PEAK 11(13Q12.13) WILD-TYPE 129  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(13Q12.13) MUTATED    244   16
  AMP PEAK 11(13Q12.13) WILD-TYPE  129   39
                               clus
vv                              AMP PEAK 11(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                    244
  COLON MUCINOUS ADENOCARCINOMA                            16
                               clus
vv                              AMP PEAK 11(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      129
  COLON MUCINOUS ADENOCARCINOMA                              39
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(13Q12.13) MUTATED     3 258
  AMP PEAK 11(13Q12.13) WILD-TYPE   0 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(13Q12.13) MUTATED      3  258
  AMP PEAK 11(13Q12.13) WILD-TYPE    0  169
     clus
vv    AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  NO                              3                               0
  YES                           258                             169
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 11(13Q12.13) MUTATED   183   1  19  10
  AMP PEAK 11(13Q12.13) WILD-TYPE 122   2   5  14
D11V10, multiclass
    clus
vv   AMP PEAK 11(13Q12.13) MUTATED AMP PEAK 11(13Q12.13) WILD-TYPE
  R0                           183                             122
  R1                             1                               2
  R2                            19                               5
  RX                            10                              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"
D11V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(13Q12.13) MUTATED                                  0     4
  AMP PEAK 11(13Q12.13) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(13Q12.13) MUTATED                          24   135
  AMP PEAK 11(13Q12.13) WILD-TYPE                        17    76
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      135
                                  clus
vv                                 AMP PEAK 11(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     17
  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(12) Variable = AMP PEAK 12(13Q22.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(13Q22.1) MUTATED   203  54
  AMP PEAK 12(13Q22.1) WILD-TYPE 126  30
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                           257                            156 
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                            54                             30 
$`AMP PEAK 12(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        5.06        37.02        46.65        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        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-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 
       15.02         5.98        37.05        19.00        85.05         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        0.99        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        32.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        26.01         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-3982 
       16.08        50.99        13.05        34.06        26.01        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       17.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.20         0.43        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.95        15.75        21.44         5.19        75.25        50.37 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        3.06         0.07         1.35        17.56       102.44        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       21.99         2.01        20.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.50        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-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-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 
       49.91        13.32         7.50       131.51         7.76         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       14.04        26.47       119.93        35.97        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         1.28         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 
       61.87        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         4.11 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         5.98         5.59        26.99        17.29 

$`AMP PEAK 12(13Q22.1) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
       19.07        33.99        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
        6.97         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99        19.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       15.95        38.99        33.07        36.03        31.07        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 
       31.00        33.01        24.00         2.01        25.02        24.00 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        21.99        34.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
        5.03         0.92        22.03        18.05        56.55         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
        0.46         0.92        27.09         0.20        17.82         5.52 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        83.80        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
      100.01         3.19         2.14         3.25         3.29         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.33         0.10        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.01         2.93       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       27.02        15.02        15.02        12.00        21.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       12.95        13.05        12.03        14.99        20.19        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        15.58        12.39         9.44        11.64         1.51 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38        44.32       135.65       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 
       13.64        13.45        35.87         1.55        16.31        19.43 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       43.07        53.62        55.04        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-QG-A5Z2 
       26.04        13.78        26.17        52.80         2.79        14.76 

  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE 
                         19.00                          21.99 
[1] "0.1 - 131.5 (19.0)" "0.1 - 140.4 (22.0)"
[1] "hr=" "1.2"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(13Q22.1) MUTATED        44        0       15        64         2
  AMP PEAK 12(13Q22.1) WILD-TYPE      28        1       13        63         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(13Q22.1) MUTATED           1        12         11         36
  AMP PEAK 12(13Q22.1) WILD-TYPE         0         9          2         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(13Q22.1) MUTATED           26       34        14         0
  AMP PEAK 12(13Q22.1) WILD-TYPE         12        8         2         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  STAGE I                              44                             28
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            64                             63
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            12                              9
  STAGE IIIA                           11                              2
  STAGE IIIB                           36                             17
  STAGE IIIC                           26                             12
  STAGE IV                             34                              8
  STAGE IVA                            14                              2
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 12(13Q22.1) MUTATED       8  47 181  29
  AMP PEAK 12(13Q22.1) WILD-TYPE     3  29 113  19
D12V4, multiclass
       clus
vv      AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  T0+T1                            8                              3
  T2                              47                             29
  T3                             181                            113
  T4                              29                             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 12(13Q22.1) MUTATED   136  75  53
  AMP PEAK 12(13Q22.1) WILD-TYPE 116  26  23
D12V5, multiclass
    clus
vv   AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  N0                          136                            116
  N1                           75                             26
  N2                           53                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 12(13Q22.1) MUTATED   187  40   7   0  28
  AMP PEAK 12(13Q22.1) WILD-TYPE 133  10   0   1  17
D12V6, multiclass
     clus
vv    AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  M0                           187                            133
  M1                            40                             10
  M1A                            7                              0
  M1B                            0                              1
  MX                            28                             17
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(13Q22.1) MUTATED   120 145
  AMP PEAK 12(13Q22.1) WILD-TYPE  83  82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(13Q22.1) MUTATED    120  145
  AMP PEAK 12(13Q22.1) WILD-TYPE   83   82
        clus
vv       AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  FEMALE                          120                             83
  MALE                            145                             82
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(13Q22.1) MUTATED   246  18
  AMP PEAK 12(13Q22.1) WILD-TYPE 127  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(13Q22.1) MUTATED    246   18
  AMP PEAK 12(13Q22.1) WILD-TYPE  127   37
                               clus
vv                              AMP PEAK 12(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   246
  COLON MUCINOUS ADENOCARCINOMA                           18
                               clus
vv                              AMP PEAK 12(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     127
  COLON MUCINOUS ADENOCARCINOMA                             37
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(13Q22.1) MUTATED     3 262
  AMP PEAK 12(13Q22.1) WILD-TYPE   0 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(13Q22.1) MUTATED      3  262
  AMP PEAK 12(13Q22.1) WILD-TYPE    0  165
     clus
vv    AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  NO                             3                              0
  YES                          262                            165
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(13Q22.1) MUTATED   185   1  18  10
  AMP PEAK 12(13Q22.1) WILD-TYPE 120   2   6  14
D12V10, multiclass
    clus
vv   AMP PEAK 12(13Q22.1) MUTATED AMP PEAK 12(13Q22.1) WILD-TYPE
  R0                          185                            120
  R1                            1                              2
  R2                           18                              6
  RX                           10                             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"
D12V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(13Q22.1) MUTATED                                  0     4
  AMP PEAK 12(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(13Q22.1) MUTATED                          25   138
  AMP PEAK 12(13Q22.1) WILD-TYPE                        16    73
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     138
                                  clus
vv                                 AMP PEAK 12(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    16
  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(13) Variable = AMP PEAK 13(16P11.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(16P11.2) MUTATED    94  20
  AMP PEAK 13(16P11.2) WILD-TYPE 235  64
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                           114                            299 
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                            20                             64 
$`AMP PEAK 13(16P11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       15.52        37.25        32.45        30.44        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       24.13        25.08        20.61        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       12.99        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3842 
       50.04        15.02        19.00        35.05        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       14.93        17.03        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98         2.01        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 
        2.01        20.98        34.03        16.08        26.01        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 
       40.96         1.02         0.10         0.20         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        0.20         5.19         5.13        62.79        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 
        1.94         2.24         3.29         1.35       102.44        48.20 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       21.99        20.02         8.02        13.02        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       16.01        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 
       15.02        11.01        10.06        19.59        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 
       15.12        17.13        12.49        10.13        13.41        11.38 
TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       38.20        13.32        35.97         8.61        13.38         1.55 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        74.56        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB 
       39.42        35.93        26.43        13.78        46.75         5.59 

$`AMP PEAK 13(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 
        5.06        46.65        43.76        23.38        42.28        13.94 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        16.04        34.65        36.53        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-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52         8.38        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-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-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        23.01        20.98        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-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        47.05        47.01        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         0.99 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       38.99         0.99        36.03        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       18.05        31.00        33.01        26.01        24.00         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        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        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         1.58         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
        0.46         0.92        14.50        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.52        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 
       21.01         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 
        8.02        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        14.99        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         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.50        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         1.28         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        43.07        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-A50V 
       26.17        91.79        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98        26.99        17.29        14.76 

  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE 
                        20.795                         19.070 
[1] "0.1 - 102.4 (20.8)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.1"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(16P11.2) MUTATED        13        1        3        29         1
  AMP PEAK 13(16P11.2) WILD-TYPE      59        0       25        98         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(16P11.2) MUTATED           0         5          9         20
  AMP PEAK 13(16P11.2) WILD-TYPE         1        16          4         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(16P11.2) MUTATED           16       15         4         0
  AMP PEAK 13(16P11.2) WILD-TYPE         22       27        12         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  STAGE I                              13                             59
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            29                             98
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              4
  STAGE IIIB                           20                             33
  STAGE IIIC                           16                             22
  STAGE IV                             15                             27
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 13(16P11.2) MUTATED       3  18  88  10
  AMP PEAK 13(16P11.2) WILD-TYPE     8  58 206  38
D13V4, multiclass
       clus
vv      AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  T0+T1                            3                              8
  T2                              18                             58
  T3                              88                            206
  T4                              10                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 13(16P11.2) MUTATED    52  36  32
  AMP PEAK 13(16P11.2) WILD-TYPE 200  65  44
D13V5, multiclass
    clus
vv   AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  N0                           52                            200
  N1                           36                             65
  N2                           32                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 13(16P11.2) MUTATED    83  16   3   0  15
  AMP PEAK 13(16P11.2) WILD-TYPE 237  34   4   1  30
D13V6, multiclass
     clus
vv    AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  M0                            83                            237
  M1                            16                             34
  M1A                            3                              4
  M1B                            0                              1
  MX                            15                             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(16P11.2) MUTATED    59  61
  AMP PEAK 13(16P11.2) WILD-TYPE 144 166
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16P11.2) MUTATED     59   61
  AMP PEAK 13(16P11.2) WILD-TYPE  144  166
        clus
vv       AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  FEMALE                           59                            144
  MALE                             61                            166
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(16P11.2) MUTATED   112   7
  AMP PEAK 13(16P11.2) WILD-TYPE 261  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16P11.2) MUTATED    112    7
  AMP PEAK 13(16P11.2) WILD-TYPE  261   48
                               clus
vv                              AMP PEAK 13(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                   112
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 13(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     261
  COLON MUCINOUS ADENOCARCINOMA                             48
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(16P11.2) MUTATED     1 119
  AMP PEAK 13(16P11.2) WILD-TYPE   2 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(16P11.2) MUTATED      1  119
  AMP PEAK 13(16P11.2) WILD-TYPE    2  308
     clus
vv    AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  NO                             1                              2
  YES                          119                            308
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(16P11.2) MUTATED    91   0   7   5
  AMP PEAK 13(16P11.2) WILD-TYPE 214   3  17  19
D13V10, multiclass
    clus
vv   AMP PEAK 13(16P11.2) MUTATED AMP PEAK 13(16P11.2) WILD-TYPE
  R0                           91                            214
  R1                            0                              3
  R2                            7                             17
  RX                            5                             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"
D13V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(16P11.2) MUTATED                                  1     3
  AMP PEAK 13(16P11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(16P11.2) MUTATED                          10    61
  AMP PEAK 13(16P11.2) WILD-TYPE                        31   150
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      61
                                  clus
vv                                 AMP PEAK 13(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    31
  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(14) Variable = AMP PEAK 14(16Q12.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(16Q12.1) MUTATED    87  14
  AMP PEAK 14(16Q12.1) WILD-TYPE 242  70
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                           101                            312 
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                            14                             70 
$`AMP PEAK 14(16Q12.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        17.79        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 
       15.52        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         1.02         0.10         0.20         0.95         0.20 
TCGA-AY-A54L TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
        5.19         5.13        62.79        29.56         5.23         1.94 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 
        3.29         1.35       102.44        48.20        21.99        20.02 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 
        8.02        22.03        22.98        16.01        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 
       29.03        21.99        14.99        15.02        11.01        10.06 
TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       19.59        18.25         1.32        15.12        17.13        12.49 
TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6459 
       10.13        13.41        11.38        38.20        35.97         8.61 
TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       13.38         1.55        82.39        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-NH-A6GB 
       39.42        35.93        26.43        13.78         5.59 

$`AMP PEAK 14(16Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2682 
        5.06        37.02        46.65        43.76        23.38        13.94 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        16.04        34.65        36.53        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-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       27.09        22.52         8.38        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        29.00         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       21.01        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       17.98        15.95        38.99         0.99        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        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        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         1.58         0.76         0.43 
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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       29.06        30.08        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-6171 
       15.02        12.00        16.04        12.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       17.75         7.92        17.85         4.50        16.14        15.58 
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-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        6.12        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        95.18        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6309 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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.06         2.79         5.98        26.99        17.29        14.76 

  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE 
                         20.98                          19.25 
[1] "0.1 - 102.4 (21.0)" "0.1 - 140.4 (19.2)"
[1] "hr=" "1.5"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(16Q12.1) MUTATED        13        1        3        22         1
  AMP PEAK 14(16Q12.1) WILD-TYPE      59        0       25       105         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(16Q12.1) MUTATED           0         5          9         20
  AMP PEAK 14(16Q12.1) WILD-TYPE         1        16          4         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(16Q12.1) MUTATED           14       11         3         0
  AMP PEAK 14(16Q12.1) WILD-TYPE         24       31        13         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  STAGE I                              13                             59
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            22                            105
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              4
  STAGE IIIB                           20                             33
  STAGE IIIC                           14                             24
  STAGE IV                             11                             31
  STAGE IVA                             3                             13
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 14(16Q12.1) MUTATED       3  18  74  10
  AMP PEAK 14(16Q12.1) WILD-TYPE     8  58 220  38
D14V4, multiclass
       clus
vv      AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  T0+T1                            3                              8
  T2                              18                             58
  T3                              74                            220
  T4                              10                             38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 14(16Q12.1) MUTATED    45  34  27
  AMP PEAK 14(16Q12.1) WILD-TYPE 207  67  49
D14V5, multiclass
    clus
vv   AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  N0                           45                            207
  N1                           34                             67
  N2                           27                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 14(16Q12.1) MUTATED    74  11   3   0  15
  AMP PEAK 14(16Q12.1) WILD-TYPE 246  39   4   1  30
D14V6, multiclass
     clus
vv    AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  M0                            74                            246
  M1                            11                             39
  M1A                            3                              4
  M1B                            0                              1
  MX                            15                             30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(16Q12.1) MUTATED    53  53
  AMP PEAK 14(16Q12.1) WILD-TYPE 150 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q12.1) MUTATED     53   53
  AMP PEAK 14(16Q12.1) WILD-TYPE  150  174
        clus
vv       AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  FEMALE                           53                            150
  MALE                             53                            174
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(16Q12.1) MUTATED    99   6
  AMP PEAK 14(16Q12.1) WILD-TYPE 274  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q12.1) MUTATED     99    6
  AMP PEAK 14(16Q12.1) WILD-TYPE  274   49
                               clus
vv                              AMP PEAK 14(16Q12.1) MUTATED
  COLON ADENOCARCINOMA                                    99
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 14(16Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     274
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(16Q12.1) MUTATED     1 105
  AMP PEAK 14(16Q12.1) WILD-TYPE   2 322
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16Q12.1) MUTATED      1  105
  AMP PEAK 14(16Q12.1) WILD-TYPE    2  322
     clus
vv    AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  NO                             1                              2
  YES                          105                            322
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(16Q12.1) MUTATED    81   0   6   4
  AMP PEAK 14(16Q12.1) WILD-TYPE 224   3  18  20
D14V10, multiclass
    clus
vv   AMP PEAK 14(16Q12.1) MUTATED AMP PEAK 14(16Q12.1) WILD-TYPE
  R0                           81                            224
  R1                            0                              3
  R2                            6                             18
  RX                            4                             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(16Q12.1) MUTATED                                  1     2
  AMP PEAK 14(16Q12.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(16Q12.1) MUTATED                           7    57
  AMP PEAK 14(16Q12.1) WILD-TYPE                        34   154
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(16Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 14(16Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  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(15) Variable = AMP PEAK 15(17P11.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(17P11.2) MUTATED    33   7
  AMP PEAK 15(17P11.2) WILD-TYPE 296  77
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                            40                            373 
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                             7                             77 
$`AMP PEAK 15(17P11.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2680 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 
        5.06        35.11        16.04        36.53        31.63        30.44 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-A56B TCGA-AA-3679 TCGA-AA-3812 
       32.71        29.16        25.08        52.44        15.02        35.05 
TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3939 TCGA-AA-3956 
        1.02        36.95        17.03         0.99        12.99        34.03 
TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-AD-6888 TCGA-AZ-5407 TCGA-AZ-6607 
        2.01        13.05        34.06         4.21        61.41         3.19 
TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6537 TCGA-D5-6924 
        1.35        29.06        14.04        11.01         4.50        14.30 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6298 
        6.12        14.04       119.93        95.18         1.55        23.51 
TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6317 
       74.56        55.04        35.93        36.00 

$`AMP PEAK 15(17P11.2) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        45.60        13.94        15.52        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         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-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-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
       85.05        26.99        19.04         0.99         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        36.03        32.05        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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3976 
        2.01        20.98        21.99        16.08        50.99        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-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-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-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        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-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        14.99        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 
        7.92        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         1.28         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        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       61.87        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         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                          0.99                           0.07 
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                        119.93                         140.38 
  AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE 
                        24.295                         19.990 
[1] "1.0 - 119.9 (24.3)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(17P11.2) MUTATED         6        0        1        14         0
  AMP PEAK 15(17P11.2) WILD-TYPE      66        1       27       113         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(17P11.2) MUTATED           1         1          1          7
  AMP PEAK 15(17P11.2) WILD-TYPE         0        20         12         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(17P11.2) MUTATED            4        5         2         0
  AMP PEAK 15(17P11.2) WILD-TYPE         34       37        14         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  STAGE I                               6                             66
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            14                            113
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             1                             20
  STAGE IIIA                            1                             12
  STAGE IIIB                            7                             46
  STAGE IIIC                            4                             34
  STAGE IV                              5                             37
  STAGE IVA                             2                             14
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 15(17P11.2) MUTATED       2   6  29   5
  AMP PEAK 15(17P11.2) WILD-TYPE     9  70 265  43
D15V4, multiclass
       clus
vv      AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  T0+T1                            2                              9
  T2                               6                             70
  T3                              29                            265
  T4                               5                             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 15(17P11.2) MUTATED    22  10   9
  AMP PEAK 15(17P11.2) WILD-TYPE 230  91  67
D15V5, multiclass
    clus
vv   AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  N0                           22                            230
  N1                           10                             91
  N2                            9                             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 15(17P11.2) MUTATED    30   5   2   0   5
  AMP PEAK 15(17P11.2) WILD-TYPE 290  45   5   1  40
D15V6, multiclass
     clus
vv    AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  M0                            30                            290
  M1                             5                             45
  M1A                            2                              5
  M1B                            0                              1
  MX                             5                             40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(17P11.2) MUTATED    18  24
  AMP PEAK 15(17P11.2) WILD-TYPE 185 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17P11.2) MUTATED     18   24
  AMP PEAK 15(17P11.2) WILD-TYPE  185  203
        clus
vv       AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  FEMALE                           18                            185
  MALE                             24                            203
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(17P11.2) MUTATED    37   5
  AMP PEAK 15(17P11.2) WILD-TYPE 336  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17P11.2) MUTATED     37    5
  AMP PEAK 15(17P11.2) WILD-TYPE  336   50
                               clus
vv                              AMP PEAK 15(17P11.2) MUTATED
  COLON ADENOCARCINOMA                                    37
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              AMP PEAK 15(17P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     336
  COLON MUCINOUS ADENOCARCINOMA                             50
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(17P11.2) MUTATED     0  42
  AMP PEAK 15(17P11.2) WILD-TYPE   3 385
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(17P11.2) MUTATED      0   42
  AMP PEAK 15(17P11.2) WILD-TYPE    3  385
     clus
vv    AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  NO                             0                              3
  YES                           42                            385
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(17P11.2) MUTATED    30   0   2   1
  AMP PEAK 15(17P11.2) WILD-TYPE 275   3  22  23
D15V10, multiclass
    clus
vv   AMP PEAK 15(17P11.2) MUTATED AMP PEAK 15(17P11.2) WILD-TYPE
  R0                           30                            275
  R1                            0                              3
  R2                            2                             22
  RX                            1                             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"
D15V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(17P11.2) MUTATED                                  1     1
  AMP PEAK 15(17P11.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(17P11.2) MUTATED                           5    22
  AMP PEAK 15(17P11.2) WILD-TYPE                        36   189
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      22
                                  clus
vv                                 AMP PEAK 15(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    36
  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(16) Variable = AMP PEAK 16(17Q12) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 16(17Q12) MUTATED    86  15
  AMP PEAK 16(17Q12) WILD-TYPE 243  69
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                         101                          312 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                          15                           69 
$`AMP PEAK 16(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 TCGA-A6-3810 
        5.06        43.76        43.43        17.79        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       14.53        30.44        29.19        32.71        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 
       25.08        25.18        24.69        20.28         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 
        1.02        58.03        38.99        36.03        29.00        12.99 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 
       24.00        23.01        15.02        36.00        85.05        35.05 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
        1.02        17.03         0.99        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3982 
       12.99        34.03         2.01        50.99        13.05        27.02 
TCGA-AA-3994 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S 
       27.02        17.03        21.99        32.02        12.00         1.02 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
        0.92        41.00         4.21         0.79         0.10         0.43 
TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
       16.31        61.41        12.10        29.56         3.19         2.24 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        0.07         1.35       102.44         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 
       13.05        11.08        11.01        19.59        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
        1.32        15.12         4.50        17.13        14.30        13.41 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 
       24.43        38.20       130.65         6.12        95.18         1.55 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       74.56        61.87        55.04        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YX 
       36.00        26.43        46.75         5.59        17.29 

$`AMP PEAK 16(17Q12) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        23.38        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
        5.03        26.99        19.04         0.99         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       14.93         0.99        33.07        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        29.98        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96         0.07        21.37        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.58         1.02         0.76         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       65.00        62.79        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         3.06         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 
       20.19        20.42        17.75         7.92        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26       119.70        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        44.68        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 
        4.11         5.06         2.79         5.98        26.99        14.76 

  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                      130.65                       140.38 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                       20.28                        19.99 
[1] "0.1 - 130.7 (20.3)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.4"
D16V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(17Q12) MUTATED        14        0        4        27         1
  AMP PEAK 16(17Q12) WILD-TYPE      58        1       24       100         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(17Q12) MUTATED           1         4          4         15
  AMP PEAK 16(17Q12) WILD-TYPE         0        17          9         38
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(17Q12) MUTATED           11       17         5         1
  AMP PEAK 16(17Q12) WILD-TYPE         27       25        11         0
D16V3, multiclass
            clus
vv           AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  STAGE I                            14                           58
  STAGE IA                            0                            1
  STAGE II                            4                           24
  STAGE IIA                          27                          100
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                           4                           17
  STAGE IIIA                          4                            9
  STAGE IIIB                         15                           38
  STAGE IIIC                         11                           27
  STAGE IV                           17                           25
  STAGE IVA                           5                           11
  STAGE IVB                           1                            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                           T0+T1  T2  T3  T4
  AMP PEAK 16(17Q12) MUTATED       5  14  77  11
  AMP PEAK 16(17Q12) WILD-TYPE     6  62 217  37
D16V4, multiclass
       clus
vv      AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  T0+T1                          5                            6
  T2                            14                           62
  T3                            77                          217
  T4                            11                           37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 16(17Q12) MUTATED    54  29  23
  AMP PEAK 16(17Q12) WILD-TYPE 198  72  53
D16V5, multiclass
    clus
vv   AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  N0                         54                          198
  N1                         29                           72
  N2                         23                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 16(17Q12) MUTATED    69  18   4   1  15
  AMP PEAK 16(17Q12) WILD-TYPE 251  32   3   0  30
D16V6, multiclass
     clus
vv    AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  M0                          69                          251
  M1                          18                           32
  M1A                          4                            3
  M1B                          1                            0
  MX                          15                           30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                              cls
clus                             0   1
  AMP PEAK 16(17Q12) MUTATED    45  62
  AMP PEAK 16(17Q12) WILD-TYPE 158 165
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     45   62
  AMP PEAK 16(17Q12) WILD-TYPE  158  165
        clus
vv       AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  FEMALE                         45                          158
  MALE                           62                          165
[1] 2 2
[1] FALSE
D16V8, binary
                              cls
clus                             0   1
  AMP PEAK 16(17Q12) MUTATED    96  10
  AMP PEAK 16(17Q12) WILD-TYPE 277  45
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     96   10
  AMP PEAK 16(17Q12) WILD-TYPE  277   45
                               clus
vv                              AMP PEAK 16(17Q12) MUTATED
  COLON ADENOCARCINOMA                                  96
  COLON MUCINOUS ADENOCARCINOMA                         10
                               clus
vv                              AMP PEAK 16(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                   277
  COLON MUCINOUS ADENOCARCINOMA                           45
[1] 2 2
[1] FALSE
D16V9, binary
                              cls
clus                             0   1
  AMP PEAK 16(17Q12) MUTATED     1 106
  AMP PEAK 16(17Q12) WILD-TYPE   2 321
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED      1  106
  AMP PEAK 16(17Q12) WILD-TYPE    2  321
     clus
vv    AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  NO                           1                            2
  YES                        106                          321
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 16(17Q12) MUTATED    71   1  10   4
  AMP PEAK 16(17Q12) WILD-TYPE 234   2  14  20
D16V10, multiclass
    clus
vv   AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  R0                         71                          234
  R1                          1                            2
  R2                         10                           14
  RX                          4                           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"
D16V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(17Q12) MUTATED                                  1     3
  AMP PEAK 16(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(17Q12) MUTATED                          11    52
  AMP PEAK 16(17Q12) WILD-TYPE                        30   159
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                11
  WHITE                                                    52
                                  clus
vv                                 AMP PEAK 16(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  30
  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(17) Variable = AMP PEAK 17(17Q24.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(17Q24.1) MUTATED    84  12
  AMP PEAK 17(17Q24.1) WILD-TYPE 245  72
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            96                            317 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            12                             72 
$`AMP PEAK 17(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-3810 
        5.06        43.43        17.79        42.28        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       14.53        30.44        29.19        32.71        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 
       25.08        25.18        24.69        20.28         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 
        1.02        58.03        24.00        23.01        15.02        36.00 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       85.05        35.05         1.02        17.03         0.99        36.03 
TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        0.99        24.03        12.99        34.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00L 
       50.99        13.05        34.06        27.02        13.94        17.03 
TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J TCGA-AA-A02O 
       21.99        12.00         1.02        37.02         5.03         0.92 
TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         4.21         0.79         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-4948 
       16.31        61.41        29.56         2.24         0.07       102.44 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 
        8.02        13.02        29.06        22.03        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       29.03        21.99        14.99        13.05        11.08        11.01 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       12.26        19.59        11.51         1.32        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M 
       17.13        14.30        13.41       130.65         6.12        95.18 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       74.56        61.87        55.04        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YX 
       36.00        26.43        91.79        46.75         5.59        17.29 

$`AMP PEAK 17(17Q24.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        43.76        23.38        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        37.05        19.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04         0.99         0.99         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 
       15.95        38.99        36.95        37.02        14.93        33.07 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 
       26.01        24.00         2.01        20.98        16.08        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02         0.99        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-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R 
       39.06        51.98         2.96        39.98         2.01        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.72         1.58         1.02         0.76         0.20         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-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-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        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.01         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02         8.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-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 
       14.99        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 
        7.92        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         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        44.68        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 
        5.06         2.79         5.98        26.99        14.76 

  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                        19.935                         19.990 
[1] "0.1 - 130.7 (19.9)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.8"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(17Q24.1) MUTATED        16        0        4        25         1
  AMP PEAK 17(17Q24.1) WILD-TYPE      56        1       24       102         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(17Q24.1) MUTATED           1         4          4         15
  AMP PEAK 17(17Q24.1) WILD-TYPE         0        17          9         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(17Q24.1) MUTATED            8       12         5         1
  AMP PEAK 17(17Q24.1) WILD-TYPE         30       30        11         0
D17V3, multiclass
            clus
vv           AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  STAGE I                              16                             56
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            25                            102
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            4                              9
  STAGE IIIB                           15                             38
  STAGE IIIC                            8                             30
  STAGE IV                             12                             30
  STAGE IVA                             5                             11
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  AMP PEAK 17(17Q24.1) MUTATED       4  17  71   7
  AMP PEAK 17(17Q24.1) WILD-TYPE     7  59 223  41
D17V4, multiclass
       clus
vv      AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  T0+T1                            4                              7
  T2                              17                             59
  T3                              71                            223
  T4                               7                             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(17Q24.1) MUTATED    55  28  15
  AMP PEAK 17(17Q24.1) WILD-TYPE 197  73  61
D17V5, multiclass
    clus
vv   AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  N0                           55                            197
  N1                           28                             73
  N2                           15                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 17(17Q24.1) MUTATED    67  13   4   1  14
  AMP PEAK 17(17Q24.1) WILD-TYPE 253  37   3   0  31
D17V6, multiclass
     clus
vv    AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  M0                            67                            253
  M1                            13                             37
  M1A                            4                              3
  M1B                            1                              0
  MX                            14                             31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q24.1) MUTATED    49  50
  AMP PEAK 17(17Q24.1) WILD-TYPE 154 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     49   50
  AMP PEAK 17(17Q24.1) WILD-TYPE  154  177
        clus
vv       AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  FEMALE                           49                            154
  MALE                             50                            177
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q24.1) MUTATED    91   7
  AMP PEAK 17(17Q24.1) WILD-TYPE 282  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     91    7
  AMP PEAK 17(17Q24.1) WILD-TYPE  282   48
                               clus
vv                              AMP PEAK 17(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                    91
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 17(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     282
  COLON MUCINOUS ADENOCARCINOMA                             48
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q24.1) MUTATED     1  98
  AMP PEAK 17(17Q24.1) WILD-TYPE   2 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED      1   98
  AMP PEAK 17(17Q24.1) WILD-TYPE    2  329
     clus
vv    AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  NO                             1                              2
  YES                           98                            329
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(17Q24.1) MUTATED    70   1   8   3
  AMP PEAK 17(17Q24.1) WILD-TYPE 235   2  16  21
D17V10, multiclass
    clus
vv   AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  R0                           70                            235
  R1                            1                              2
  R2                            8                             16
  RX                            3                             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(17Q24.1) MUTATED                                  0     2
  AMP PEAK 17(17Q24.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q24.1) MUTATED                          10    51
  AMP PEAK 17(17Q24.1) WILD-TYPE                        31   160
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      51
                                  clus
vv                                 AMP PEAK 17(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    31
  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(18) Variable = AMP PEAK 18(19P13.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(19P13.2) MUTATED    53  13
  AMP PEAK 18(19P13.2) WILD-TYPE 276  71
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                            66                            347 
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                            13                             71 
$`AMP PEAK 18(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 
        5.06        37.02        43.43        44.91        45.60        15.52 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 
       36.53        14.53        31.63        29.16        25.18        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3685 
       23.87        52.44         9.07         6.05         2.01        37.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3994 
       35.05         0.99        31.07        50.99        13.05        27.02 
TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 
       13.94        42.02        32.02        51.98         0.92         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 
        1.02         0.43         0.46        16.31        61.41        29.56 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 
       11.74         3.06         1.35        40.34        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
        8.02        13.02        29.06        16.01         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6676 
       15.02        14.04        29.03        21.99        13.02        11.08 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A28F 
       19.59        13.51        15.12        11.38        49.91        35.97 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6627 
       74.56        45.11        39.42        36.00        26.43        47.15 

$`AMP PEAK 18(19P13.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        23.38        17.79        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 
       13.94        37.05        37.25        16.04        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04         0.99         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07         7.96        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.20         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       61.87        53.62        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.98         5.59        26.99        17.29        14.76 

  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                         74.56                         140.38 
  AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE 
                        21.875                         19.990 
[1] "0.4 - 74.6 (21.9)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1"  
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(19P13.2) MUTATED         9        0        4        18         1
  AMP PEAK 18(19P13.2) WILD-TYPE      63        1       24       109         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(19P13.2) MUTATED           0         5          3         13
  AMP PEAK 18(19P13.2) WILD-TYPE         1        16         10         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(19P13.2) MUTATED            4        7         4         0
  AMP PEAK 18(19P13.2) WILD-TYPE         34       35        12         1
D18V3, multiclass
            clus
vv           AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            18                            109
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            3                             10
  STAGE IIIB                           13                             40
  STAGE IIIC                            4                             34
  STAGE IV                              7                             35
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 18(19P13.2) MUTATED       2   9  51   8
  AMP PEAK 18(19P13.2) WILD-TYPE     9  67 243  40
D18V4, multiclass
       clus
vv      AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  T0+T1                            2                              9
  T2                               9                             67
  T3                              51                            243
  T4                               8                             40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 18(19P13.2) MUTATED    35  26   9
  AMP PEAK 18(19P13.2) WILD-TYPE 217  75  67
D18V5, multiclass
    clus
vv   AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  N0                           35                            217
  N1                           26                             75
  N2                            9                             67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 18(19P13.2) MUTATED    45   8   3   0  13
  AMP PEAK 18(19P13.2) WILD-TYPE 275  42   4   1  32
D18V6, multiclass
     clus
vv    AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  M0                            45                            275
  M1                             8                             42
  M1A                            3                              4
  M1B                            0                              1
  MX                            13                             32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.2) MUTATED    25  45
  AMP PEAK 18(19P13.2) WILD-TYPE 178 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.2) MUTATED     25   45
  AMP PEAK 18(19P13.2) WILD-TYPE  178  182
        clus
vv       AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  FEMALE                           25                            178
  MALE                             45                            182
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.2) MUTATED    64   6
  AMP PEAK 18(19P13.2) WILD-TYPE 309  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.2) MUTATED     64    6
  AMP PEAK 18(19P13.2) WILD-TYPE  309   49
                               clus
vv                              AMP PEAK 18(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                    64
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 18(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     309
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(19P13.2) MUTATED     1  69
  AMP PEAK 18(19P13.2) WILD-TYPE   2 358
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(19P13.2) MUTATED      1   69
  AMP PEAK 18(19P13.2) WILD-TYPE    2  358
     clus
vv    AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  NO                             1                              2
  YES                           69                            358
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(19P13.2) MUTATED    48   2   3   6
  AMP PEAK 18(19P13.2) WILD-TYPE 257   1  21  18
D18V10, multiclass
    clus
vv   AMP PEAK 18(19P13.2) MUTATED AMP PEAK 18(19P13.2) WILD-TYPE
  R0                           48                            257
  R1                            2                              1
  R2                            3                             21
  RX                            6                             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"
D18V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(19P13.2) MUTATED                                  0     2
  AMP PEAK 18(19P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(19P13.2) MUTATED                           8    42
  AMP PEAK 18(19P13.2) WILD-TYPE                        33   169
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      42
                                  clus
vv                                 AMP PEAK 18(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    33
  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(19) Variable = AMP PEAK 19(19Q13.11) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(19Q13.11) MUTATED    69  15
  AMP PEAK 19(19Q13.11) WILD-TYPE 260  69
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                             84                             329 
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                             15                              69 
$`AMP PEAK 19(19Q13.11) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2686 
        5.06        37.02        43.43        45.60        15.52        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 
       34.65        36.53        14.53        31.63        29.16        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 
       25.18        21.76        23.87        61.84        52.44        35.01 
TCGA-AA-3506 TCGA-AA-3522 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 TCGA-AA-3812 
       58.03        37.05        12.99        13.02        37.05        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 TCGA-AA-3972 
        0.99        37.02        33.07        36.03        12.99        50.99 
TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01G 
       13.05        18.05        27.02        42.02        21.99        12.00 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 
       51.98        39.98         0.92         4.21         1.58         1.02 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-5407 TCGA-AZ-6603 
        0.43        14.50         0.20         5.52        61.41        29.56 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 
       11.74         3.06         1.35        40.34        21.99         2.01 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 
       37.02         8.02        13.02        29.06        16.01         5.03 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 
       15.02        15.02        14.04        29.03        21.99        11.08 
TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       19.59        15.12         4.50        11.64        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 
       11.38       119.70        35.97         8.61        13.64        35.41 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 
       82.39        74.56        45.11        39.42        26.43        47.15 

$`AMP PEAK 19(19Q13.11) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        23.38        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       35.11        13.94        37.05        37.25        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       32.71        27.09        22.52        24.13         8.38        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05         1.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01         0.99        14.01        33.99        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-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-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 
       85.05        26.99        19.04         0.99         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-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        17.03         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
       33.04        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.01         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 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         1.32         7.92        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         9.04         9.44         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
      119.93        60.79       117.07        98.24        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6569 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         1.28         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        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6321 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-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.98         5.59        26.99        17.29        14.76 

  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                           0.20                            0.07 
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE 
                          21.99                           19.66 
[1] "0.2 - 119.7 (22.0)" "0.1 - 140.4 (19.7)"
[1] "hr=" "1.2"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(19Q13.11) MUTATED        12        0        4        27         0
  AMP PEAK 19(19Q13.11) WILD-TYPE      60        1       24       100         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(19Q13.11) MUTATED           0         3          4         14
  AMP PEAK 19(19Q13.11) WILD-TYPE         1        18          9         39
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(19Q13.11) MUTATED            8       11         4         0
  AMP PEAK 19(19Q13.11) WILD-TYPE         30       31        12         1
D19V3, multiclass
            clus
vv           AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  STAGE I                               12                              60
  STAGE IA                               0                               1
  STAGE II                               4                              24
  STAGE IIA                             27                             100
  STAGE IIB                              0                               8
  STAGE IIC                              0                               1
  STAGE III                              3                              18
  STAGE IIIA                             4                               9
  STAGE IIIB                            14                              39
  STAGE IIIC                             8                              30
  STAGE IV                              11                              31
  STAGE IVA                              4                              12
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 19(19Q13.11) MUTATED       2  14  65   8
  AMP PEAK 19(19Q13.11) WILD-TYPE     9  62 229  40
D19V4, multiclass
       clus
vv      AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  T0+T1                             2                               9
  T2                               14                              62
  T3                               65                             229
  T4                                8                              40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 19(19Q13.11) MUTATED    46  29  13
  AMP PEAK 19(19Q13.11) WILD-TYPE 206  72  63
D19V5, multiclass
    clus
vv   AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  N0                            46                             206
  N1                            29                              72
  N2                            13                              63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 19(19Q13.11) MUTATED    60  11   4   0  13
  AMP PEAK 19(19Q13.11) WILD-TYPE 260  39   3   1  32
D19V6, multiclass
     clus
vv    AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  M0                             60                             260
  M1                             11                              39
  M1A                             4                               3
  M1B                             0                               1
  MX                             13                              32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(19Q13.11) MUTATED    34  55
  AMP PEAK 19(19Q13.11) WILD-TYPE 169 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(19Q13.11) MUTATED     34   55
  AMP PEAK 19(19Q13.11) WILD-TYPE  169  172
        clus
vv       AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  FEMALE                            34                             169
  MALE                              55                             172
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                                0   1
  AMP PEAK 19(19Q13.11) MUTATED    80   9
  AMP PEAK 19(19Q13.11) WILD-TYPE 293  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(19Q13.11) MUTATED     80    9
  AMP PEAK 19(19Q13.11) WILD-TYPE  293   46
                               clus
vv                              AMP PEAK 19(19Q13.11) MUTATED
  COLON ADENOCARCINOMA                                     80
  COLON MUCINOUS ADENOCARCINOMA                             9
                               clus
vv                              AMP PEAK 19(19Q13.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      293
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(19Q13.11) MUTATED     1  88
  AMP PEAK 19(19Q13.11) WILD-TYPE   2 339
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(19Q13.11) MUTATED      1   88
  AMP PEAK 19(19Q13.11) WILD-TYPE    2  339
     clus
vv    AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  NO                              1                               2
  YES                            88                             339
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(19Q13.11) MUTATED    65   1   4   6
  AMP PEAK 19(19Q13.11) WILD-TYPE 240   2  20  18
D19V10, multiclass
    clus
vv   AMP PEAK 19(19Q13.11) MUTATED AMP PEAK 19(19Q13.11) WILD-TYPE
  R0                            65                             240
  R1                             1                               2
  R2                             4                              20
  RX                             6                              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"
D19V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(19Q13.11) MUTATED                                  0     2
  AMP PEAK 19(19Q13.11) WILD-TYPE                                1     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(19Q13.11) MUTATED                           9    52
  AMP PEAK 19(19Q13.11) WILD-TYPE                        32   159
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 19(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     32
  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(20) Variable = AMP PEAK 20(20P11.23) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(20P11.23) MUTATED   158  45
  AMP PEAK 20(20P11.23) WILD-TYPE 171  39
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                            203                             210 
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                             45                              39 
$`AMP PEAK 20(20P11.23) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        15.52        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6137 
       36.53        14.53        32.45        30.44        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        24.16        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3496 
       61.84         9.63         5.03         1.02         1.02         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       58.03         6.97         1.02        19.07        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 
       14.01        21.01        13.02        23.01        20.98        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 
       37.05        19.00        36.00         5.03         0.99         0.99 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
        0.99        31.07        17.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       13.05        26.01        24.00        27.02        19.07         7.96 
TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W 
       13.94        18.05        17.03         4.01        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S 
       21.99        15.02         0.99        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       33.04        26.01        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 
        5.03         0.92        41.00        39.98         0.07        21.37 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4323 
        0.43        14.50        16.31         5.19         5.52         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-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       48.20        20.02         8.02         8.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 
       14.04        29.03        16.04        21.99        14.04        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        11.01        14.99        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       20.19        17.75        17.85        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 
       10.13         9.04        11.64        13.41        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 
       24.43       130.65        12.59         7.50       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
        6.12        14.04       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 
        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-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.72        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
       47.15         4.11         5.59        26.99        17.29 

$`AMP PEAK 20(20P11.23) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 
       46.65        23.38        42.28        37.05        37.25        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       32.71        22.52        24.13         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       24.39        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 
        3.02        37.05        35.01        63.98        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-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
       19.07        34.03        26.01        12.99         0.99        33.99 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       24.00        17.95        29.95        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 
       78.08         6.97        54.02         0.92        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.98        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3854 
       25.02         1.02        17.98        15.95        36.95        36.03 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 
       32.05        31.07        53.00        24.03        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       34.06        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       15.02        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J 
       35.01        37.02        39.06        22.03        18.05        40.96 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        4.21        56.55         0.76         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 
        0.95        15.75         0.20        21.44        17.82        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
       50.37        58.39         5.65        32.94        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01         5.23        11.74         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
        0.10       102.44        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-4746 
       21.01         2.93         2.01       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.03        30.08        16.01        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 
       12.00        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-D5-6530 
       13.05        11.08        10.06        12.03        13.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6540 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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67         1.28         0.53        19.43 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 
       44.68        51.75        36.00        26.43        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       26.17        52.80         5.06         2.79         5.98        14.76 

  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE 
                         17.030                          22.785 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (22.8)"
[1] "hr=" "1.4"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(20P11.23) MUTATED        34        1       11        54         3
  AMP PEAK 20(20P11.23) WILD-TYPE      38        0       17        73         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(20P11.23) MUTATED           0         9         12         20
  AMP PEAK 20(20P11.23) WILD-TYPE         1        12          1         33
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(20P11.23) MUTATED           17       33        10         0
  AMP PEAK 20(20P11.23) WILD-TYPE         21        9         6         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  STAGE I                               34                              38
  STAGE IA                               1                               0
  STAGE II                              11                              17
  STAGE IIA                             54                              73
  STAGE IIB                              3                               5
  STAGE IIC                              0                               1
  STAGE III                              9                              12
  STAGE IIIA                            12                               1
  STAGE IIIB                            20                              33
  STAGE IIIC                            17                              21
  STAGE IV                              33                               9
  STAGE IVA                             10                               6
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 20(20P11.23) MUTATED       5  38 145  22
  AMP PEAK 20(20P11.23) WILD-TYPE     6  38 149  26
D20V4, multiclass
       clus
vv      AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  T0+T1                             5                               6
  T2                               38                              38
  T3                              145                             149
  T4                               22                              26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 20(20P11.23) MUTATED   113  59  39
  AMP PEAK 20(20P11.23) WILD-TYPE 139  42  37
D20V5, multiclass
    clus
vv   AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  N0                           113                             139
  N1                            59                              42
  N2                            39                              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 20(20P11.23) MUTATED   142  35   7   0  25
  AMP PEAK 20(20P11.23) WILD-TYPE 178  15   0   1  20
D20V6, multiclass
     clus
vv    AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  M0                            142                             178
  M1                             35                              15
  M1A                             7                               0
  M1B                             0                               1
  MX                             25                              20
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20P11.23) MUTATED    95 116
  AMP PEAK 20(20P11.23) WILD-TYPE 108 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20P11.23) MUTATED     95  116
  AMP PEAK 20(20P11.23) WILD-TYPE  108  111
        clus
vv       AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  FEMALE                            95                             108
  MALE                             116                             111
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20P11.23) MUTATED   192  18
  AMP PEAK 20(20P11.23) WILD-TYPE 181  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20P11.23) MUTATED    192   18
  AMP PEAK 20(20P11.23) WILD-TYPE  181   37
                               clus
vv                              AMP PEAK 20(20P11.23) MUTATED
  COLON ADENOCARCINOMA                                    192
  COLON MUCINOUS ADENOCARCINOMA                            18
                               clus
vv                              AMP PEAK 20(20P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      181
  COLON MUCINOUS ADENOCARCINOMA                              37
[1] 2 2
[1] FALSE
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20P11.23) MUTATED     3 208
  AMP PEAK 20(20P11.23) WILD-TYPE   0 219
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20P11.23) MUTATED      3  208
  AMP PEAK 20(20P11.23) WILD-TYPE    0  219
     clus
vv    AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  NO                              3                               0
  YES                           208                             219
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(20P11.23) MUTATED   140   2  19  11
  AMP PEAK 20(20P11.23) WILD-TYPE 165   1   5  13
D20V10, multiclass
    clus
vv   AMP PEAK 20(20P11.23) MUTATED AMP PEAK 20(20P11.23) WILD-TYPE
  R0                           140                             165
  R1                             2                               1
  R2                            19                               5
  RX                            11                              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"
D20V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(20P11.23) MUTATED                                  1     7
  AMP PEAK 20(20P11.23) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(20P11.23) MUTATED                          17   105
  AMP PEAK 20(20P11.23) WILD-TYPE                        24   106
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(20P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      105
                                  clus
vv                                 AMP PEAK 20(20P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     24
  WHITE                                                        106
[1] 4 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(20Q11.21) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(20Q11.21) MUTATED   237  59
  AMP PEAK 21(20Q11.21) WILD-TYPE  92  25
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            296                             117 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                             59                              25 
$`AMP PEAK 21(20Q11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
        0.99        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.95        15.75         0.20         5.19         5.52        75.25 
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-6607 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        2.01        20.02        37.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.50        17.13        12.49         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.43        14.30         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       23.51        61.87        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         4.11         5.06         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX 
       26.99        17.29 

$`AMP PEAK 21(20Q11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 
       29.95        61.02         6.97        54.02         0.92        11.01 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        19.04         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        53.00        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        24.00         2.01        25.02        27.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q 
       30.02        18.05         0.99        34.98        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
       35.01        35.01        39.06        22.03        18.05        56.55 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
        0.76         0.92        27.09        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         5.65        32.94        61.41         6.77       100.01 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
       11.74         3.25         0.33         0.10        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       51.32        21.01         2.93       124.27        23.05        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       27.02        15.02        12.00        12.95        13.05        12.03 
TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       20.42        16.14        15.58         9.44         1.51        12.00 
TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      140.38       135.65         7.76        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 
       11.11        35.87        16.31        19.43        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       53.62        51.75        22.09        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
        2.79         5.98        14.76 

  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                         18.625                          22.090 
[1] "0.1 - 139.2 (18.6)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1.1"
D21V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20Q11.21) MUTATED        51        1       16        82         3
  AMP PEAK 21(20Q11.21) WILD-TYPE      21        0       12        45         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20Q11.21) MUTATED           1        14         13         37
  AMP PEAK 21(20Q11.21) WILD-TYPE         0         7          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(20Q11.21) MUTATED           30       37        15         0
  AMP PEAK 21(20Q11.21) WILD-TYPE          8        5         1         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  STAGE I                               51                              21
  STAGE IA                               1                               0
  STAGE II                              16                              12
  STAGE IIA                             82                              45
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             14                               7
  STAGE IIIA                            13                               0
  STAGE IIIB                            37                              16
  STAGE IIIC                            30                               8
  STAGE IV                              37                               5
  STAGE IVA                             15                               1
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 21(20Q11.21) MUTATED       7  57 213  29
  AMP PEAK 21(20Q11.21) WILD-TYPE     4  19  81  19
D21V4, multiclass
       clus
vv      AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  T0+T1                             7                               4
  T2                               57                              19
  T3                              213                              81
  T4                               29                              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 21(20Q11.21) MUTATED   167  81  58
  AMP PEAK 21(20Q11.21) WILD-TYPE  85  20  18
D21V5, multiclass
    clus
vv   AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  N0                           167                              85
  N1                            81                              20
  N2                            58                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 21(20Q11.21) MUTATED   220  44   7   0  32
  AMP PEAK 21(20Q11.21) WILD-TYPE 100   6   0   1  13
D21V6, multiclass
     clus
vv    AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  M0                            220                             100
  M1                             44                               6
  M1A                             7                               0
  M1B                             0                               1
  MX                             32                              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED   140 167
  AMP PEAK 21(20Q11.21) WILD-TYPE  63  60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED    140  167
  AMP PEAK 21(20Q11.21) WILD-TYPE   63   60
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  FEMALE                           140                              63
  MALE                             167                              60
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED   281  24
  AMP PEAK 21(20Q11.21) WILD-TYPE  92  31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED    281   24
  AMP PEAK 21(20Q11.21) WILD-TYPE   92   31
                               clus
vv                              AMP PEAK 21(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                    281
  COLON MUCINOUS ADENOCARCINOMA                            24
                               clus
vv                              AMP PEAK 21(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       92
  COLON MUCINOUS ADENOCARCINOMA                              31
[1] 2 2
[1] FALSE
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED     3 304
  AMP PEAK 21(20Q11.21) WILD-TYPE   0 123
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED      3  304
  AMP PEAK 21(20Q11.21) WILD-TYPE    0  123
     clus
vv    AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  NO                              3                               0
  YES                           304                             123
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(20Q11.21) MUTATED   215   2  21  14
  AMP PEAK 21(20Q11.21) WILD-TYPE  90   1   3  10
D21V10, multiclass
    clus
vv   AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  R0                           215                              90
  R1                             2                               1
  R2                            21                               3
  RX                            14                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(20Q11.21) MUTATED                                  1     7
  AMP PEAK 21(20Q11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20Q11.21) MUTATED                          28   154
  AMP PEAK 21(20Q11.21) WILD-TYPE                        13    57
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      154
                                  clus
vv                                 AMP PEAK 21(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     13
  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(22) Variable = AMP PEAK 22(20Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(20Q12) MUTATED   238  59
  AMP PEAK 22(20Q12) WILD-TYPE  91  25
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                         297                          116 
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                          59                           25 
$`AMP PEAK 22(20Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       35.05         0.99        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        19.07         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        17.03         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         0.46        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
        0.20         5.19         5.52        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-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        48.20        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         8.02         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        14.99 
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         7.92        15.12        17.85         4.50 
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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       39.42        35.93        36.72        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       13.78        91.79        46.75        47.15         4.11         5.06 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59        26.99        17.29 

$`AMP PEAK 22(20Q12) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 
       29.95        61.02         6.97        54.02         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         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       15.95        36.03        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D 
       38.04        30.02        18.05         0.99        34.98         0.99 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R 
       38.07         1.02        35.01        35.01        39.06        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       18.05        56.55         0.76         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       17.82        50.37        58.39        32.94        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
      100.01        11.74         3.25         0.33         0.10        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 
       26.04        27.02        15.02        12.00        12.95        13.05 
TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 
       12.03        20.42        16.14        15.58         9.44         1.51 
TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G 
       12.00       140.38       135.65         7.76        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 
       98.24        11.11        35.87        19.43        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       51.75        22.09        35.80        26.17        52.80         2.79 
TCGA-NH-A6GA TCGA-QG-A5Z2 
        5.98        14.76 

  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                        0.07                         0.10 
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                      139.17                       140.38 
  AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE 
                       19.00                        22.09 
[1] "0.1 - 139.2 (19.0)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1"  
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20Q12) MUTATED        51        1       16        83         3
  AMP PEAK 22(20Q12) WILD-TYPE      21        0       12        44         5
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20Q12) MUTATED           1        13         13         37
  AMP PEAK 22(20Q12) WILD-TYPE         0         8          0         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20Q12) MUTATED           30       37        16         0
  AMP PEAK 22(20Q12) WILD-TYPE          8        5         0         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  STAGE I                            51                           21
  STAGE IA                            1                            0
  STAGE II                           16                           12
  STAGE IIA                          83                           44
  STAGE IIB                           3                            5
  STAGE IIC                           1                            0
  STAGE III                          13                            8
  STAGE IIIA                         13                            0
  STAGE IIIB                         37                           16
  STAGE IIIC                         30                            8
  STAGE IV                           37                            5
  STAGE IVA                          16                            0
  STAGE IVB                           0                            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                           T0+T1  T2  T3  T4
  AMP PEAK 22(20Q12) MUTATED       7  57 213  30
  AMP PEAK 22(20Q12) WILD-TYPE     4  19  81  18
D22V4, multiclass
       clus
vv      AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  T0+T1                          7                            4
  T2                            57                           19
  T3                           213                           81
  T4                            30                           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 22(20Q12) MUTATED   168  81  58
  AMP PEAK 22(20Q12) WILD-TYPE  84  20  18
D22V5, multiclass
    clus
vv   AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  N0                        168                           84
  N1                         81                           20
  N2                         58                           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"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 22(20Q12) MUTATED   220  45   7   0  32
  AMP PEAK 22(20Q12) WILD-TYPE 100   5   0   1  13
D22V6, multiclass
     clus
vv    AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  M0                         220                          100
  M1                          45                            5
  M1A                          7                            0
  M1B                          0                            1
  MX                          32                           13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(20Q12) MUTATED   140 168
  AMP PEAK 22(20Q12) WILD-TYPE  63  59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(20Q12) MUTATED    140  168
  AMP PEAK 22(20Q12) WILD-TYPE   63   59
        clus
vv       AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  FEMALE                        140                           63
  MALE                          168                           59
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(20Q12) MUTATED   283  23
  AMP PEAK 22(20Q12) WILD-TYPE  90  32
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(20Q12) MUTATED    283   23
  AMP PEAK 22(20Q12) WILD-TYPE   90   32
                               clus
vv                              AMP PEAK 22(20Q12) MUTATED
  COLON ADENOCARCINOMA                                 283
  COLON MUCINOUS ADENOCARCINOMA                         23
                               clus
vv                              AMP PEAK 22(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                           32
[1] 2 2
[1] FALSE
D22V9, binary
                              cls
clus                             0   1
  AMP PEAK 22(20Q12) MUTATED     3 305
  AMP PEAK 22(20Q12) WILD-TYPE   0 122
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(20Q12) MUTATED      3  305
  AMP PEAK 22(20Q12) WILD-TYPE    0  122
     clus
vv    AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  NO                           3                            0
  YES                        305                          122
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(20Q12) MUTATED   216   2  21  14
  AMP PEAK 22(20Q12) WILD-TYPE  89   1   3  10
D22V10, multiclass
    clus
vv   AMP PEAK 22(20Q12) MUTATED AMP PEAK 22(20Q12) WILD-TYPE
  R0                        216                           89
  R1                          2                            1
  R2                         21                            3
  RX                         14                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20Q12) MUTATED                                  1     7
  AMP PEAK 22(20Q12) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q12) MUTATED                          28   157
  AMP PEAK 22(20Q12) WILD-TYPE                        13    54
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                28
  WHITE                                                   157
                                  clus
vv                                 AMP PEAK 22(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  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(23) Variable = AMP PEAK 23(20Q13.32) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20Q13.32) MUTATED   240  60
  AMP PEAK 23(20Q13.32) WILD-TYPE  89  24
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                            300                             113 
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                             60                              24 
$`AMP PEAK 23(20Q13.32) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 
       85.05         0.99        35.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05        12.99        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 
       26.01        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
        0.99        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        1.02         0.10         0.20         0.43         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         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         1.41         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         1.35        17.56       102.44        40.34 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       48.20        21.99         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       13.02        15.02        14.04        11.01        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.50        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       131.51       139.17         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        13.78        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
       47.15         4.11         5.06         5.59        26.99        17.29 

$`AMP PEAK 23(20Q13.32) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3710 
       29.95        61.02         6.97         0.92        11.01        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 
       19.04         0.99         1.02        17.98        15.95        36.03 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        27.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       18.05         0.99        34.98        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         0.76 
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-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 
        5.65        32.94        61.41         6.77       100.01         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        21.01 
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        43.07        53.62        51.75        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       26.17        52.80         2.79         5.98        14.76 

  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE 
                         18.625                          22.090 
[1] "0.1 - 139.2 (18.6)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1"  
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q13.32) MUTATED        51        1       17        83         3
  AMP PEAK 23(20Q13.32) WILD-TYPE      21        0       11        44         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q13.32) MUTATED           1        14         13         37
  AMP PEAK 23(20Q13.32) WILD-TYPE         0         7          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20Q13.32) MUTATED           31       38        15         0
  AMP PEAK 23(20Q13.32) WILD-TYPE          7        4         1         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  STAGE I                               51                              21
  STAGE IA                               1                               0
  STAGE II                              17                              11
  STAGE IIA                             83                              44
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             14                               7
  STAGE IIIA                            13                               0
  STAGE IIIB                            37                              16
  STAGE IIIC                            31                               7
  STAGE IV                              38                               4
  STAGE IVA                             15                               1
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 23(20Q13.32) MUTATED       7  57 216  30
  AMP PEAK 23(20Q13.32) WILD-TYPE     4  19  78  18
D23V4, multiclass
       clus
vv      AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  T0+T1                             7                               4
  T2                               57                              19
  T3                              216                              78
  T4                               30                              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 23(20Q13.32) MUTATED   169  81  60
  AMP PEAK 23(20Q13.32) WILD-TYPE  83  20  16
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  N0                           169                              83
  N1                            81                              20
  N2                            60                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 23(20Q13.32) MUTATED   223  45   7   0  32
  AMP PEAK 23(20Q13.32) WILD-TYPE  97   5   0   1  13
D23V6, multiclass
     clus
vv    AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  M0                            223                              97
  M1                             45                               5
  M1A                             7                               0
  M1B                             0                               1
  MX                             32                              13
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.32) MUTATED   142 169
  AMP PEAK 23(20Q13.32) WILD-TYPE  61  58
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.32) MUTATED    142  169
  AMP PEAK 23(20Q13.32) WILD-TYPE   61   58
        clus
vv       AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  FEMALE                           142                              61
  MALE                             169                              58
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.32) MUTATED   285  24
  AMP PEAK 23(20Q13.32) WILD-TYPE  88  31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.32) MUTATED    285   24
  AMP PEAK 23(20Q13.32) WILD-TYPE   88   31
                               clus
vv                              AMP PEAK 23(20Q13.32) MUTATED
  COLON ADENOCARCINOMA                                    285
  COLON MUCINOUS ADENOCARCINOMA                            24
                               clus
vv                              AMP PEAK 23(20Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       88
  COLON MUCINOUS ADENOCARCINOMA                              31
[1] 2 2
[1] FALSE
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.32) MUTATED     3 308
  AMP PEAK 23(20Q13.32) WILD-TYPE   0 119
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.32) MUTATED      3  308
  AMP PEAK 23(20Q13.32) WILD-TYPE    0  119
     clus
vv    AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  NO                              3                               0
  YES                           308                             119
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20Q13.32) MUTATED   218   2  21  14
  AMP PEAK 23(20Q13.32) WILD-TYPE  87   1   3  10
D23V10, multiclass
    clus
vv   AMP PEAK 23(20Q13.32) MUTATED AMP PEAK 23(20Q13.32) WILD-TYPE
  R0                           218                              87
  R1                             2                               1
  R2                            21                               3
  RX                            14                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(20Q13.32) MUTATED                                  1     7
  AMP PEAK 23(20Q13.32) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20Q13.32) MUTATED                          28   157
  AMP PEAK 23(20Q13.32) WILD-TYPE                        13    54
D23V12, multiclass
                                  clus
vv                                 AMP PEAK 23(20Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      157
                                  clus
vv                                 AMP PEAK 23(20Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     13
  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(24) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   119  37
  DEL PEAK  1(1P36.11) WILD-TYPE 210  47
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           156                            257 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            37                             47 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        17.79        44.91        35.11        13.94        15.52 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       36.53        14.53        32.45        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       29.16        22.52        24.13        25.18        21.76        23.87 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 
       52.44         5.03        38.99         9.07        37.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       19.07        34.03        14.01        13.02        24.00        23.01 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       19.99         2.01        14.01        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 
       19.00        36.00        85.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 
       31.07        31.07        17.03        24.03        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       12.99         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       26.01         7.96        34.03        42.02        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03        41.00        40.96         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
        5.52         5.65         5.13        22.36        65.00        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
        3.29         0.07         0.26         1.35        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02         8.02        13.02        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       15.02        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        10.06        12.03        14.99        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6541 
       17.75         1.32         7.92        15.12        17.85        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.43        14.30        13.41        11.38        92.75        49.91 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28M 
       44.32       139.17         6.12        26.47       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 
       13.38        11.11         1.55        29.59         1.28        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 
        8.35        82.39        23.51        61.87        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       36.00        91.79        46.75         4.11         5.98        26.99 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        37.02        46.65        43.43        23.38        42.28 
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 
       45.60        37.05        37.25        16.04        34.65        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       31.63        30.44        33.53        22.09        22.06        27.09 
TCGA-A6-6141 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-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 
        1.02        24.03        36.03         8.05        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01        12.99         0.99        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
        6.05         6.97        54.02         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-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-3846 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       17.03        36.03        53.00        27.02        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       16.08        34.06        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        17.03         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        21.99        34.98         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37         4.21        56.55         0.72         0.10 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.76         0.92        27.09         0.95        15.75         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94        83.80        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01        11.74         1.94         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        26.04        27.02        29.06        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       16.04        21.99        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       20.42        18.25         4.50        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        7.53        12.39        10.13         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65         7.76        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6856 
       35.87        16.31        16.24        33.67         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      107.67        28.21        74.56        43.07        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 
       55.04        51.75        45.11        39.42        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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.06         2.79         5.59        17.29        14.76 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         17.82                          20.61 
[1] "0.1 - 139.2 (17.8)" "0.1 - 140.4 (20.6)"
[1] "hr=" "1.5"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.11) MUTATED        21        0        5        44         1
  DEL PEAK  1(1P36.11) WILD-TYPE      51        1       23        83         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1         8          5         18
  DEL PEAK  1(1P36.11) WILD-TYPE         0        13          8         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           17       28         9         0
  DEL PEAK  1(1P36.11) WILD-TYPE         21       14         7         1
D24V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              21                             51
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            44                             83
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            5                              8
  STAGE IIIB                           18                             35
  STAGE IIIC                           17                             21
  STAGE IV                             28                             14
  STAGE IVA                             9                              7
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED       3  26 113  19
  DEL PEAK  1(1P36.11) WILD-TYPE     8  50 181  29
D24V4, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                            3                              8
  T2                              26                             50
  T3                             113                            181
  T4                              19                             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
  DEL PEAK  1(1P36.11) MUTATED    81  42  38
  DEL PEAK  1(1P36.11) WILD-TYPE 171  59  38
D24V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           81                            171
  N1                           42                             59
  N2                           38                             38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  1(1P36.11) MUTATED   105  34   3   0  18
  DEL PEAK  1(1P36.11) WILD-TYPE 215  16   4   1  27
D24V6, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           105                            215
  M1                            34                             16
  M1A                            3                              4
  M1B                            0                              1
  MX                            18                             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    70  91
  DEL PEAK  1(1P36.11) WILD-TYPE 133 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     70   91
  DEL PEAK  1(1P36.11) WILD-TYPE  133  136
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           70                            133
  MALE                             91                            136
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   150  10
  DEL PEAK  1(1P36.11) WILD-TYPE 223  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    150   10
  DEL PEAK  1(1P36.11) WILD-TYPE  223   45
                               clus
vv                              DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                   150
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                     223
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D24V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     1 160
  DEL PEAK  1(1P36.11) WILD-TYPE   2 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      1  160
  DEL PEAK  1(1P36.11) WILD-TYPE    2  267
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             1                              2
  YES                          160                            267
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   106   1  14  11
  DEL PEAK  1(1P36.11) WILD-TYPE 199   2  10  13
D24V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          106                            199
  R1                            1                              2
  R2                           14                             10
  RX                           11                             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"
D24V11, 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                          13    79
  DEL PEAK  1(1P36.11) WILD-TYPE                        28   132
D24V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    28
  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(25) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED    82  30
  DEL PEAK  2(1P33) WILD-TYPE 247  54
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        112                         301 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         30                          54 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       43.76        35.11        15.52        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 
       14.53        32.45        29.19        23.61        29.16        22.52 
TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       21.76        23.87         5.03        38.99         9.07        37.05 
TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 
        8.05        21.01        19.99        50.04        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       85.05         0.99        38.99        36.95        37.02         0.99 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 
       33.07        32.05        31.07        17.03        24.03         2.01 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F 
       12.99         2.01        21.99        13.05         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       42.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        22.03        41.00         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D 
        1.02         0.20         0.43        14.50        16.31         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.65         5.13        62.79        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 
        3.19         2.24         3.06         2.14         0.26         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
        8.02        13.02        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6924 TCGA-D5-6929 
       13.51         1.32        15.12        17.85        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A288 TCGA-DM-A28A 
       11.38        38.20        92.75        49.91        14.04        26.47 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       35.97        13.38         1.55        35.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       23.51        61.87        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75         4.11         5.98        26.99 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-3807 
       42.28        44.91        45.60        13.94        37.05        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-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        24.13         8.38        25.08        25.18 
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-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       24.03        36.03        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-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-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 
       17.98        15.95        14.93        17.03        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         5.03         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37         4.21        56.55         0.72         0.10 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.76         0.46         0.92        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.20        21.44        17.82         5.19        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        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.01         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         8.02        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 
       14.99        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         7.92         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 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         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43       107.67        28.21        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX 
       47.15        52.80         5.06         2.79         5.59        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      92.75                      140.38 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      16.67                       20.28 
[1] "0.2 - 92.8 (16.7)"  "0.1 - 140.4 (20.3)"
[1] "hr=" "1.8"
D25V2, 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      60        1       23        93         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         6          3         15
  DEL PEAK  2(1P33) WILD-TYPE         1        15         10         38
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           14       21         3         0
  DEL PEAK  2(1P33) WILD-TYPE         24       21        13         1
D25V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           12                          60
  STAGE IA                           0                           1
  STAGE II                           5                          23
  STAGE IIA                         34                          93
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          6                          15
  STAGE IIIA                         3                          10
  STAGE IIIB                        15                          38
  STAGE IIIC                        14                          24
  STAGE IV                          21                          21
  STAGE IVA                          3                          13
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  DEL PEAK  2(1P33) MUTATED       3  15  85  14
  DEL PEAK  2(1P33) WILD-TYPE     8  61 209  34
D25V4, multiclass
       clus
vv      DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T0+T1                         3                           8
  T2                           15                          61
  T3                           85                         209
  T4                           14                          34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK  2(1P33) MUTATED    56  32  29
  DEL PEAK  2(1P33) WILD-TYPE 196  69  47
D25V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        56                         196
  N1                        32                          69
  N2                        29                          47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  2(1P33) MUTATED    76  23   1   0  17
  DEL PEAK  2(1P33) WILD-TYPE 244  27   6   1  28
D25V6, multiclass
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  M0                         76                         244
  M1                         23                          27
  M1A                         1                           6
  M1B                         0                           1
  MX                         17                          28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    53  64
  DEL PEAK  2(1P33) WILD-TYPE 150 163
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     53   64
  DEL PEAK  2(1P33) WILD-TYPE  150  163
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        53                         150
  MALE                          64                         163
[1] 2 2
[1] FALSE
D25V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   108   9
  DEL PEAK  2(1P33) WILD-TYPE 265  46
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    108    9
  DEL PEAK  2(1P33) WILD-TYPE  265   46
                               clus
vv                              DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                108
  COLON MUCINOUS ADENOCARCINOMA                         9
                               clus
vv                              DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                  265
  COLON MUCINOUS ADENOCARCINOMA                          46
[1] 2 2
[1] FALSE
D25V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     0 117
  DEL PEAK  2(1P33) WILD-TYPE   3 310
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      0  117
  DEL PEAK  2(1P33) WILD-TYPE    3  310
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          0                           3
  YES                       117                         310
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED    75   1  10   7
  DEL PEAK  2(1P33) WILD-TYPE 230   2  14  17
D25V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        75                         230
  R1                         1                           2
  R2                        10                          14
  RX                         7                          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"
D25V11, 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                          13    57
  DEL PEAK  2(1P33) WILD-TYPE                        28   154
D25V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               13
  WHITE                                                   57
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 28
  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(26) Variable = DEL PEAK  3(1P13.1) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.1) MUTATED    83  25
  DEL PEAK  3(1P13.1) WILD-TYPE 246  59
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          108                           305 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                           25                            59 
$`DEL PEAK  3(1P13.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3810 
       37.02        43.76        35.11        15.52        37.25        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 
       14.53        32.45        29.19        23.61        22.52        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       23.87        52.44         5.03        38.99         9.07        37.05 
TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 
       21.01        13.94        19.99        50.04        37.05        19.00 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 
        0.99        38.99        37.02         0.99        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 
       17.03        24.03         2.01        12.99         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q TCGA-AA-A01C 
       21.99        13.05         7.96        38.04        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       32.02        31.00         1.02        33.04        26.01         2.96 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 
        2.01        41.00        40.96         0.79         1.02         0.20 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4615 TCGA-AZ-4616 
        0.43         0.92        14.50         5.52        32.94         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-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
        3.06         2.14         0.26         2.01         8.02        13.02 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       22.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       10.06        13.51        17.75         1.32        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 
       13.41        11.38        92.75        49.91       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6855 
       14.04        26.47        13.38         1.55        16.24        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
        8.35        82.39        23.51        61.87        36.72        36.00 
TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       26.04        91.79        46.75         4.11         5.98        26.99 

$`DEL PEAK  3(1P13.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 
       44.91        45.60        13.94        37.05        16.04        34.65 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 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-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        36.95        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
       33.07        36.03         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       29.98        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 
       24.00        20.98        34.03        16.08        50.99        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       13.94        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 
        1.58         0.10         0.76         0.46        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41         5.65        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-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       11.74         1.94         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.26        19.59        11.51        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 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-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
        7.50        44.32       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       16.31        29.59        33.67         1.28         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      107.67        28.21        74.56        43.07        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       55.04        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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.06         2.79         5.59        17.29        14.76 

  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                         0.20                          0.07 
  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 
                       16.635                        20.280 
[1] "0.2 - 131.5 (16.6)" "0.1 - 140.4 (20.3)"
[1] "hr=" "1.4"
D26V2, 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      60        1       23        96         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.1) MUTATED           0         5          3         15
  DEL PEAK  3(1P13.1) WILD-TYPE         1        16         10         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.1) MUTATED           13       22         2         0
  DEL PEAK  3(1P13.1) WILD-TYPE         25       20        14         1
D26V3, multiclass
            clus
vv           DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  STAGE I                             12                            60
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           31                            96
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           3                            10
  STAGE IIIB                          15                            38
  STAGE IIIC                          13                            25
  STAGE IV                            22                            20
  STAGE IVA                            2                            14
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  3(1P13.1) MUTATED       3  15  82  12
  DEL PEAK  3(1P13.1) WILD-TYPE     8  61 212  36
D26V4, multiclass
       clus
vv      DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  T0+T1                           3                             8
  T2                             15                            61
  T3                             82                           212
  T4                             12                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK  3(1P13.1) MUTATED    52  30  30
  DEL PEAK  3(1P13.1) WILD-TYPE 200  71  46
D26V5, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  N0                          52                           200
  N1                          30                            71
  N2                          30                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  3(1P13.1) MUTATED    73  24   0   0  15
  DEL PEAK  3(1P13.1) WILD-TYPE 247  26   7   1  30
D26V6, multiclass
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  M0                           73                           247
  M1                           24                            26
  M1A                           0                             7
  M1B                           0                             1
  MX                           15                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    49  63
  DEL PEAK  3(1P13.1) WILD-TYPE 154 164
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     49   63
  DEL PEAK  3(1P13.1) WILD-TYPE  154  164
        clus
vv       DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  FEMALE                          49                           154
  MALE                            63                           164
[1] 2 2
[1] FALSE
D26V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED   103   9
  DEL PEAK  3(1P13.1) WILD-TYPE 270  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED    103    9
  DEL PEAK  3(1P13.1) WILD-TYPE  270   46
                               clus
vv                              DEL PEAK  3(1P13.1) MUTATED
  COLON ADENOCARCINOMA                                  103
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK  3(1P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    270
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D26V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED     1 111
  DEL PEAK  3(1P13.1) WILD-TYPE   2 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED      1  111
  DEL PEAK  3(1P13.1) WILD-TYPE    2  316
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  NO                            1                             2
  YES                         111                           316
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.1) MUTATED    71   0  10   8
  DEL PEAK  3(1P13.1) WILD-TYPE 234   3  14  16
D26V10, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  R0                          71                           234
  R1                           0                             3
  R2                          10                            14
  RX                           8                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, 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                          13    54
  DEL PEAK  3(1P13.1) WILD-TYPE                        28   157
D26V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK  3(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   28
  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(27) Variable = DEL PEAK  4(1Q43) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q43) MUTATED    41   8
  DEL PEAK  4(1Q43) WILD-TYPE 288  76
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         49                         364 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                          8                          76 
$`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         1.02 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 
        0.20         0.43        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        48.20         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 
       91.79 

$`DEL PEAK  4(1Q43) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       14.53        32.45        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-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-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-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        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         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-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        17.03         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 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-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         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94        83.80        22.36        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-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-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        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 
       26.04        27.02        13.02        29.06        22.98        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-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-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        18.25         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        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-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-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-F4-6809 
        6.18        35.87        16.31        29.59        16.24         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       55.04        51.75        45.11        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        26.99        17.29        14.76 

  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                       0.20                        0.07 
  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 
                     15.020                      20.515 
[1] "0.2 - 91.8 (15.0)"  "0.1 - 140.4 (20.5)"
[1] "hr=" "1.1"
D27V2, 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      61        1       26       117         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          8         50
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(1Q43) MUTATED            6        8         0         0
  DEL PEAK  4(1Q43) WILD-TYPE         32       34        16         1
D27V3, multiclass
            clus
vv           DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  STAGE I                           11                          61
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                         10                         117
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          2                          19
  STAGE IIIA                         5                           8
  STAGE IIIB                         3                          50
  STAGE IIIC                         6                          32
  STAGE IV                           8                          34
  STAGE IVA                          0                          16
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  DEL PEAK  4(1Q43) MUTATED       3  13  30   5
  DEL PEAK  4(1Q43) WILD-TYPE     8  63 264  43
D27V4, multiclass
       clus
vv      DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  T0+T1                         3                           8
  T2                           13                          63
  T3                           30                         264
  T4                            5                          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  4(1Q43) MUTATED    26  13  12
  DEL PEAK  4(1Q43) WILD-TYPE 226  88  64
D27V5, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  N0                        26                         226
  N1                        13                          88
  N2                        12                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  4(1Q43) MUTATED    33   8   0   0  10
  DEL PEAK  4(1Q43) WILD-TYPE 287  42   7   1  35
D27V6, multiclass
     clus
vv    DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  M0                         33                         287
  M1                          8                          42
  M1A                         0                           7
  M1B                         0                           1
  MX                         10                          35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    23  28
  DEL PEAK  4(1Q43) WILD-TYPE 180 199
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     23   28
  DEL PEAK  4(1Q43) WILD-TYPE  180  199
        clus
vv       DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  FEMALE                        23                         180
  MALE                          28                         199
[1] 2 2
[1] FALSE
D27V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    46   5
  DEL PEAK  4(1Q43) WILD-TYPE 327  50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     46    5
  DEL PEAK  4(1Q43) WILD-TYPE  327   50
                               clus
vv                              DEL PEAK  4(1Q43) MUTATED
  COLON ADENOCARCINOMA                                 46
  COLON MUCINOUS ADENOCARCINOMA                         5
                               clus
vv                              DEL PEAK  4(1Q43) WILD-TYPE
  COLON ADENOCARCINOMA                                  327
  COLON MUCINOUS ADENOCARCINOMA                          50
[1] 2 2
[1] FALSE
D27V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED     1  50
  DEL PEAK  4(1Q43) WILD-TYPE   2 377
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED      1   50
  DEL PEAK  4(1Q43) WILD-TYPE    2  377
     clus
vv    DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  NO                          1                           2
  YES                        50                         377
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q43) MUTATED    31   1   3   3
  DEL PEAK  4(1Q43) WILD-TYPE 274   2  21  21
D27V10, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  R0                        31                         274
  R1                         1                           2
  R2                         3                          21
  RX                         3                          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"
D27V11, 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                           4    31
  DEL PEAK  4(1Q43) WILD-TYPE                        37   180
D27V12, multiclass
                                  clus
vv                                 DEL PEAK  4(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   31
                                  clus
vv                                 DEL PEAK  4(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 37
  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(28) Variable = DEL PEAK  5(2P21) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(2P21) MUTATED    14   2
  DEL PEAK  5(2P21) WILD-TYPE 315  82
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         397 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                          2                          82 
$`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 
        7.92        11.38        11.11         5.06 

$`DEL PEAK  5(2P21) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-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-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-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         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-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        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-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         1.58         1.02         0.10         0.76         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.25         3.29         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.01         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        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-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25         1.32        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 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-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                       1.02                        0.07 
  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 
                     12.185                      20.120 
[1] "1.0 - 50.4 (12.2)"  "0.1 - 140.4 (20.1)"
[1] "hr=" "1.3"
D28V2, 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      70        1       26       124         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         11         51
                             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         34       42        16         1
D28V3, multiclass
            clus
vv           DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  STAGE I                            2                          70
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                          3                         124
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          1                          20
  STAGE IIIA                         2                          11
  STAGE IIIB                         2                          51
  STAGE IIIC                         4                          34
  STAGE IV                           0                          42
  STAGE IVA                          0                          16
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  DEL PEAK  5(2P21) MUTATED       1   3  10   2
  DEL PEAK  5(2P21) WILD-TYPE    10  73 284  46
D28V4, multiclass
       clus
vv      DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  T0+T1                         1                          10
  T2                            3                          73
  T3                           10                         284
  T4                            2                          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  5(2P21) MUTATED     7   4   5
  DEL PEAK  5(2P21) WILD-TYPE 245  97  71
D28V5, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  N0                         7                         245
  N1                         4                          97
  N2                         5                          71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  5(2P21) MUTATED    16   0   0   0   0
  DEL PEAK  5(2P21) WILD-TYPE 304  50   7   1  45
D28V6, multiclass
     clus
vv    DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  M0                         16                         304
  M1                          0                          50
  M1A                         0                           7
  M1B                         0                           1
  MX                          0                          45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     9   7
  DEL PEAK  5(2P21) WILD-TYPE 194 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      9    7
  DEL PEAK  5(2P21) WILD-TYPE  194  220
        clus
vv       DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  FEMALE                         9                         194
  MALE                           7                         220
[1] 2 2
[1] FALSE
D28V8, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED    15   1
  DEL PEAK  5(2P21) WILD-TYPE 358  54
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     15    1
  DEL PEAK  5(2P21) WILD-TYPE  358   54
                               clus
vv                              DEL PEAK  5(2P21) MUTATED
  COLON ADENOCARCINOMA                                 15
  COLON MUCINOUS ADENOCARCINOMA                         1
                               clus
vv                              DEL PEAK  5(2P21) WILD-TYPE
  COLON ADENOCARCINOMA                                  358
  COLON MUCINOUS ADENOCARCINOMA                          54
[1] 2 2
[1] FALSE
D28V9, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     0  16
  DEL PEAK  5(2P21) WILD-TYPE   3 411
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      0   16
  DEL PEAK  5(2P21) WILD-TYPE    3  411
     clus
vv    DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  NO                          0                           3
  YES                        16                         411
[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 290   3  24  24
D28V10, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  R0                        15                         290
  R1                         0                           3
  R2                         0                          24
  RX                         0                          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"
D28V11, 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                        39   205
D28V12, 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                                 39
  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(29) Variable = DEL PEAK  6(2Q32.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q32.1) MUTATED    10   3
  DEL PEAK  6(2Q32.1) WILD-TYPE 319  81
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                           13                           400 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                            3                            81 
$`DEL PEAK  6(2Q32.1) MUTATED`
TCGA-A6-6648 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3842 
       25.18         6.97        37.05        19.99         2.01        37.02 
TCGA-AA-3848 TCGA-AA-3939 TCGA-AA-3977 TCGA-AA-A01K TCGA-CA-5797 TCGA-DM-A1D6 
        0.99        12.99        25.02        31.00         3.29        49.91 
TCGA-F4-6460 
       13.38 

$`DEL PEAK  6(2Q32.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.08        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-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-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-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       36.95        14.93        17.03        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        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-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        26.99        17.29        14.76 

  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                        49.91                        140.38 
  DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE 
                       19.990                        20.005 
[1] "1.0 - 49.9 (20.0)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1.4"
D29V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(2Q32.1) MUTATED         0        0        1         4         0
  DEL PEAK  6(2Q32.1) WILD-TYPE      72        1       27       123         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q32.1) MUTATED           0         1          1          1
  DEL PEAK  6(2Q32.1) WILD-TYPE         1        20         12         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(2Q32.1) MUTATED            3        1         1         0
  DEL PEAK  6(2Q32.1) WILD-TYPE         35       41        15         1
D29V3, multiclass
            clus
vv           DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  STAGE I                              0                            72
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                            4                           123
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            12
  STAGE IIIB                           1                            52
  STAGE IIIC                           3                            35
  STAGE IV                             1                            41
  STAGE IVA                            1                            15
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  6(2Q32.1) MUTATED       0   2  10   2
  DEL PEAK  6(2Q32.1) WILD-TYPE    11  74 284  46
D29V4, multiclass
       clus
vv      DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  T0+T1                           0                            11
  T2                              2                            74
  T3                             10                           284
  T4                              2                            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  6(2Q32.1) MUTATED     7   4   3
  DEL PEAK  6(2Q32.1) WILD-TYPE 245  97  73
D29V5, multiclass
    clus
vv   DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  N0                           7                           245
  N1                           4                            97
  N2                           3                            73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  6(2Q32.1) MUTATED    11   1   1   0   0
  DEL PEAK  6(2Q32.1) WILD-TYPE 309  49   6   1  45
D29V6, multiclass
     clus
vv    DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  M0                           11                           309
  M1                            1                            49
  M1A                           1                             6
  M1B                           0                             1
  MX                            0                            45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED     5   9
  DEL PEAK  6(2Q32.1) WILD-TYPE 198 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED      5    9
  DEL PEAK  6(2Q32.1) WILD-TYPE  198  218
        clus
vv       DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  FEMALE                           5                           198
  MALE                             9                           218
[1] 2 2
[1] FALSE
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED    13   1
  DEL PEAK  6(2Q32.1) WILD-TYPE 360  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED     13    1
  DEL PEAK  6(2Q32.1) WILD-TYPE  360   54
                               clus
vv                              DEL PEAK  6(2Q32.1) MUTATED
  COLON ADENOCARCINOMA                                   13
  COLON MUCINOUS ADENOCARCINOMA                           1
                               clus
vv                              DEL PEAK  6(2Q32.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    360
  COLON MUCINOUS ADENOCARCINOMA                            54
[1] 2 2
[1] FALSE
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q32.1) MUTATED     0  14
  DEL PEAK  6(2Q32.1) WILD-TYPE   3 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q32.1) MUTATED      0   14
  DEL PEAK  6(2Q32.1) WILD-TYPE    3  413
     clus
vv    DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  NO                            0                             3
  YES                          14                           413
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q32.1) MUTATED    10   0   1   0
  DEL PEAK  6(2Q32.1) WILD-TYPE 295   3  23  24
D29V10, multiclass
    clus
vv   DEL PEAK  6(2Q32.1) MUTATED DEL PEAK  6(2Q32.1) WILD-TYPE
  R0                          10                           295
  R1                           0                             3
  R2                           1                            23
  RX                           0                            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"
D29V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q32.1) MUTATED                                  0     1
  DEL PEAK  6(2Q32.1) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q32.1) MUTATED                           0     3
  DEL PEAK  6(2Q32.1) WILD-TYPE                        41   208
D29V12, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      3
                                  clus
vv                                 DEL PEAK  6(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      208
[1] 4 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  7(3P26.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.1) MUTATED    52  13
  DEL PEAK  7(3P26.1) WILD-TYPE 277  71
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           65                           348 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                           13                            71 
$`DEL PEAK  7(3P26.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       43.43        15.52        34.65        36.53        14.53        32.45 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 
       29.16        22.52        25.08        21.76         9.63         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3662 TCGA-AA-3679 
        6.97        38.99         9.07        29.00         6.05        15.02 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3870 
       85.05         0.99        32.05        31.07        17.03        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3979 
        2.01        12.99         2.01        21.99        50.99        24.00 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02H 
        7.96        13.94        27.02        32.02        31.00         2.01 
TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6607 
        0.43         0.20         5.65         5.13        12.10         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        3.29         0.26         2.01         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 
       22.03         5.03        14.04        11.08        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6929 
       17.75         1.32         7.92        15.12        17.85        13.41 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV 
       11.38         7.50        13.38         5.98        26.99 

$`DEL PEAK  7(3P26.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       42.28        44.91        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.25        16.04        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        52.44         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-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-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        33.07        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        24.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       16.08        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-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        48.20        51.32        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-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        14.99        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         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 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         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        4.11         5.06         2.79         5.59        17.29        14.76 

  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE 
                        13.94                         21.01 
[1] "0.2 - 85.0 (13.9)"  "0.1 - 140.4 (21.0)"
[1] "hr=" "1.5"
D30V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P26.1) MUTATED         6        0        1        18         0
  DEL PEAK  7(3P26.1) WILD-TYPE      66        1       27       109         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.1) MUTATED           0         4          2         10
  DEL PEAK  7(3P26.1) WILD-TYPE         1        17         11         43
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.1) MUTATED            7       14         4         0
  DEL PEAK  7(3P26.1) WILD-TYPE         31       28        12         1
D30V3, multiclass
            clus
vv           DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  STAGE I                              6                            66
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           18                           109
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           2                            11
  STAGE IIIB                          10                            43
  STAGE IIIC                           7                            31
  STAGE IV                            14                            28
  STAGE IVA                            4                            12
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  7(3P26.1) MUTATED       2   6  48  10
  DEL PEAK  7(3P26.1) WILD-TYPE     9  70 246  38
D30V4, multiclass
       clus
vv      DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  T0+T1                           2                             9
  T2                              6                            70
  T3                             48                           246
  T4                             10                            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  7(3P26.1) MUTATED    28  21  17
  DEL PEAK  7(3P26.1) WILD-TYPE 224  80  59
D30V5, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  N0                          28                           224
  N1                          21                            80
  N2                          17                            59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  7(3P26.1) MUTATED    40  15   3   0   7
  DEL PEAK  7(3P26.1) WILD-TYPE 280  35   4   1  38
D30V6, multiclass
     clus
vv    DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  M0                           40                           280
  M1                           15                            35
  M1A                           3                             4
  M1B                           0                             1
  MX                            7                            38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED    31  35
  DEL PEAK  7(3P26.1) WILD-TYPE 172 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED     31   35
  DEL PEAK  7(3P26.1) WILD-TYPE  172  192
        clus
vv       DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  FEMALE                          31                           172
  MALE                            35                           192
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED    62   4
  DEL PEAK  7(3P26.1) WILD-TYPE 311  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED     62    4
  DEL PEAK  7(3P26.1) WILD-TYPE  311   51
                               clus
vv                              DEL PEAK  7(3P26.1) MUTATED
  COLON ADENOCARCINOMA                                   62
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK  7(3P26.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    311
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.1) MUTATED     0  66
  DEL PEAK  7(3P26.1) WILD-TYPE   3 361
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.1) MUTATED      0   66
  DEL PEAK  7(3P26.1) WILD-TYPE    3  361
     clus
vv    DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  NO                            0                             3
  YES                          66                           361
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.1) MUTATED    46   0   7   4
  DEL PEAK  7(3P26.1) WILD-TYPE 259   3  17  20
D30V10, multiclass
    clus
vv   DEL PEAK  7(3P26.1) MUTATED DEL PEAK  7(3P26.1) WILD-TYPE
  R0                          46                           259
  R1                           0                             3
  R2                           7                            17
  RX                           4                            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"
D30V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P26.1) MUTATED                                  0     2
  DEL PEAK  7(3P26.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P26.1) MUTATED                           6    32
  DEL PEAK  7(3P26.1) WILD-TYPE                        35   179
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     32
                                  clus
vv                                 DEL PEAK  7(3P26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   35
  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(31) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.2) MUTATED    62  16
  DEL PEAK  8(3P14.2) WILD-TYPE 267  68
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           78                           335 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           16                            68 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       15.52        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-A56B 
       29.16        22.52        25.08        21.76        20.12        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3662 
        9.63         5.03        38.99         1.02         9.07         6.05 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       54.02         0.92        11.01        37.05        85.05         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 
       32.05        31.07        17.03         2.01        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00J 
       21.99        24.00        27.02         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02W 
       17.03        27.02         0.99        32.02        31.00        41.00 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       21.37         0.79         1.58         0.43         0.46        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-6600 TCGA-CA-5797 
       16.31         0.20        75.25         5.65        12.10         3.29 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6171 
        0.26         2.01         8.02         5.03        14.04        14.04 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       13.05        11.08        11.01        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1DA 
        7.92        17.85        13.41        11.38       119.70         7.50 
TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 TCGA-NH-A6GA TCGA-QG-A5YV 
       35.97       117.07        13.38        36.00         5.98        26.99 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.05        37.25        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       61.84         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        15.02         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        53.00        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        26.01        25.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05         4.01        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       22.03        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.02         0.10         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        5.19         5.52        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.01         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-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-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       13.51        11.51        20.42        18.25        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        12.00        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       26.47        81.37       119.93        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6320 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         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.06         2.79         5.59        17.29        14.76 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.20                          0.07 
  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 
                       14.515                        21.440 
[1] "0.2 - 119.7 (14.5)" "0.1 - 140.4 (21.4)"
[1] "hr=" "1.3"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3P14.2) MUTATED        10        0        2        22         0
  DEL PEAK  8(3P14.2) WILD-TYPE      62        1       26       105         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED           0         5          1         13
  DEL PEAK  8(3P14.2) WILD-TYPE         1        16         12         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3P14.2) MUTATED           11       10         5         1
  DEL PEAK  8(3P14.2) WILD-TYPE         27       32        11         0
D31V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                             10                            62
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           22                           105
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           1                            12
  STAGE IIIB                          13                            40
  STAGE IIIC                          11                            27
  STAGE IV                            10                            32
  STAGE IVA                            5                            11
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK  8(3P14.2) MUTATED       3   9  56  13
  DEL PEAK  8(3P14.2) WILD-TYPE     8  67 238  35
D31V4, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                           3                             8
  T2                              9                            67
  T3                             56                           238
  T4                             13                            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  8(3P14.2) MUTATED    38  23  20
  DEL PEAK  8(3P14.2) WILD-TYPE 214  78  56
D31V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          38                           214
  N1                          23                            78
  N2                          20                            56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  8(3P14.2) MUTATED    55  12   3   1   9
  DEL PEAK  8(3P14.2) WILD-TYPE 265  38   4   0  36
D31V6, multiclass
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                           55                           265
  M1                           12                            38
  M1A                           3                             4
  M1B                           1                             0
  MX                            9                            36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    41  40
  DEL PEAK  8(3P14.2) WILD-TYPE 162 187
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     41   40
  DEL PEAK  8(3P14.2) WILD-TYPE  162  187
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          41                           162
  MALE                            40                           187
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    74   7
  DEL PEAK  8(3P14.2) WILD-TYPE 299  48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     74    7
  DEL PEAK  8(3P14.2) WILD-TYPE  299   48
                               clus
vv                              DEL PEAK  8(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                   74
  COLON MUCINOUS ADENOCARCINOMA                           7
                               clus
vv                              DEL PEAK  8(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    299
  COLON MUCINOUS ADENOCARCINOMA                            48
[1] 2 2
[1] FALSE
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED     0  81
  DEL PEAK  8(3P14.2) WILD-TYPE   3 346
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      0   81
  DEL PEAK  8(3P14.2) WILD-TYPE    3  346
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                            0                             3
  YES                          81                           346
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P14.2) MUTATED    57   1   6   3
  DEL PEAK  8(3P14.2) WILD-TYPE 248   2  18  21
D31V10, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                          57                           248
  R1                           1                             2
  R2                           6                            18
  RX                           3                            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"
D31V11, 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                           8    39
  DEL PEAK  8(3P14.2) WILD-TYPE                        33   172
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     39
                                  clus
vv                                 DEL PEAK  8(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   33
  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(32) Variable = DEL PEAK  9(3Q26.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(3Q26.31) MUTATED    37   7
  DEL PEAK  9(3Q26.31) WILD-TYPE 292  77
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            369 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             7                             77 
$`DEL PEAK  9(3Q26.31) MUTATED`
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5666 TCGA-A6-A56B TCGA-AA-3517 
       34.65        14.53        32.45        32.71        52.44        38.99 
TCGA-AA-3519 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 
        9.07        19.99         6.05        85.05         0.99        32.05 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A01F 
       12.99         2.01        21.99         7.96        13.94        32.02 
TCGA-AA-A01T TCGA-AA-A02R TCGA-AD-A5EK TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-5254 
       33.04        22.03         0.43        58.39        12.10         2.24 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 
        0.26         0.10        13.02         5.03        11.08        11.01 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 
       13.51        20.19         1.32         7.92        17.85        13.41 
TCGA-D5-6932 TCGA-DM-A1HA TCGA-DM-A282 TCGA-F4-6460 TCGA-G4-6297 TCGA-G4-6317 
       11.38       131.51       139.17        13.38        82.39        36.00 
TCGA-NH-A50T TCGA-QG-A5YV 
        4.11        26.99 

$`DEL PEAK  9(3Q26.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5656 
       15.52        37.05        37.25        16.04        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-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-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-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-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-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-3994 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07        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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        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-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-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        50.37         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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.33         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04         8.02        27.02        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-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        19.59        11.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76         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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 
       35.41        19.43       107.67        28.21         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        17.29        14.76 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        13.725                         20.420 
[1] "0.1 - 139.2 (13.7)" "0.1 - 140.4 (20.4)"
[1] "hr=" "1.3"
D32V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(3Q26.31) MUTATED         3        0        0        19         0
  DEL PEAK  9(3Q26.31) WILD-TYPE      69        1       28       108         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q26.31) MUTATED           1         4          0          5
  DEL PEAK  9(3Q26.31) WILD-TYPE         0        17         13         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(3Q26.31) MUTATED            5        5         2         0
  DEL PEAK  9(3Q26.31) WILD-TYPE         33       37        14         1
D32V3, multiclass
            clus
vv           DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  STAGE I                               3                             69
  STAGE IA                              0                              1
  STAGE II                              0                             28
  STAGE IIA                            19                            108
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            0                             13
  STAGE IIIB                            5                             48
  STAGE IIIC                            5                             33
  STAGE IV                              5                             37
  STAGE IVA                             2                             14
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK  9(3Q26.31) MUTATED       0   3  35   6
  DEL PEAK  9(3Q26.31) WILD-TYPE    11  73 259  42
D32V4, multiclass
       clus
vv      DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T0+T1                            0                             11
  T2                               3                             73
  T3                              35                            259
  T4                               6                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  9(3Q26.31) MUTATED    25  11   8
  DEL PEAK  9(3Q26.31) WILD-TYPE 227  90  68
D32V5, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                           25                            227
  N1                           11                             90
  N2                            8                             68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  9(3Q26.31) MUTATED    33   5   2   0   4
  DEL PEAK  9(3Q26.31) WILD-TYPE 287  45   5   1  41
D32V6, multiclass
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  M0                            33                            287
  M1                             5                             45
  M1A                            2                              5
  M1B                            0                              1
  MX                             4                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    20  24
  DEL PEAK  9(3Q26.31) WILD-TYPE 183 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     20   24
  DEL PEAK  9(3Q26.31) WILD-TYPE  183  203
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                           20                            183
  MALE                             24                            203
[1] 2 2
[1] FALSE
D32V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    42   2
  DEL PEAK  9(3Q26.31) WILD-TYPE 331  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     42    2
  DEL PEAK  9(3Q26.31) WILD-TYPE  331   53
                               clus
vv                              DEL PEAK  9(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                    42
  COLON MUCINOUS ADENOCARCINOMA                            2
                               clus
vv                              DEL PEAK  9(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                     331
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D32V9, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED     0  44
  DEL PEAK  9(3Q26.31) WILD-TYPE   3 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      0   44
  DEL PEAK  9(3Q26.31) WILD-TYPE    3  383
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  NO                             0                              3
  YES                           44                            383
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(3Q26.31) MUTATED    33   0   2   3
  DEL PEAK  9(3Q26.31) WILD-TYPE 272   3  22  21
D32V10, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  R0                           33                            272
  R1                            0                              3
  R2                            2                             22
  RX                            3                             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  9(3Q26.31) MUTATED                                  0     3
  DEL PEAK  9(3Q26.31) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q26.31) MUTATED                           6    20
  DEL PEAK  9(3Q26.31) WILD-TYPE                        35   191
D32V12, multiclass
                                  clus
vv                                 DEL PEAK  9(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      20
                                  clus
vv                                 DEL PEAK  9(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK 10(4P16.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4P16.2) MUTATED    91  32
  DEL PEAK 10(4P16.2) WILD-TYPE 238  52
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          123                           290 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                           32                            52 
$`DEL PEAK 10(4P16.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 
       37.05        16.04        14.53        32.45        30.44        29.16 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       25.18        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
        9.63         5.03         1.02        38.99        37.05        34.03 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 
       12.99        21.01        13.02        19.99         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
        2.01        50.04        15.02        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       29.98         2.01        12.99         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       21.99        50.99        26.01        34.03        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        2.01        41.00         1.58         1.02         0.20        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
        0.95        15.75         0.20         5.52         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 
       65.00        12.10        29.56         3.19         2.14         3.29 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5864 
       48.20         8.02        29.06        22.03        22.98        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 
       17.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.01        10.06        14.99        13.51        20.19        17.75 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA 
       14.30         9.04        13.41        11.38        12.59         7.50 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
        6.12        14.04        26.47         1.55        16.24        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
       35.41         8.35        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-QG-A5YV 
       46.75         4.11        26.99 

$`DEL PEAK 10(4P16.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.25        34.65        36.53        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-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-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        36.03         8.05        19.07        19.07 
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-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       13.94        61.02        78.08         6.97        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       36.03        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        24.00        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        21.44        17.82         5.19 
TCGA-AZ-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-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-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-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 
       21.01         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-5349 
       37.02         8.02        26.04        27.02        13.02        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02         5.03        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       12.95        13.05        11.08        12.03        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.42        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 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-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 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-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.31        29.59         1.28         0.53        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        82.39        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        51.75        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         5.06         2.79         5.98         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                         0.20                          0.07 
  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 
                       19.990                        20.005 
[1] "0.2 - 91.8 (20.0)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1.7"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4P16.2) MUTATED        15        0        6        29         2
  DEL PEAK 10(4P16.2) WILD-TYPE      57        1       22        98         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4P16.2) MUTATED           0         5          7         14
  DEL PEAK 10(4P16.2) WILD-TYPE         1        16          6         39
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4P16.2) MUTATED           15       25         6         0
  DEL PEAK 10(4P16.2) WILD-TYPE         23       17        10         1
D33V3, multiclass
            clus
vv           DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  STAGE I                             15                            57
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           29                            98
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           7                             6
  STAGE IIIB                          14                            39
  STAGE IIIC                          15                            23
  STAGE IV                            25                            17
  STAGE IVA                            6                            10
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 10(4P16.2) MUTATED       4  19  88  17
  DEL PEAK 10(4P16.2) WILD-TYPE     7  57 206  31
D33V4, multiclass
       clus
vv      DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  T0+T1                           4                             7
  T2                             19                            57
  T3                             88                           206
  T4                             17                            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 10(4P16.2) MUTATED    57  38  33
  DEL PEAK 10(4P16.2) WILD-TYPE 195  63  43
D33V5, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  N0                          57                           195
  N1                          38                            63
  N2                          33                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 10(4P16.2) MUTATED    79  28   3   0  14
  DEL PEAK 10(4P16.2) WILD-TYPE 241  22   4   1  31
D33V6, multiclass
     clus
vv    DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  M0                           79                           241
  M1                           28                            22
  M1A                           3                             4
  M1B                           0                             1
  MX                           14                            31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED    58  70
  DEL PEAK 10(4P16.2) WILD-TYPE 145 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED     58   70
  DEL PEAK 10(4P16.2) WILD-TYPE  145  157
        clus
vv       DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  FEMALE                          58                           145
  MALE                            70                           157
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED   118   9
  DEL PEAK 10(4P16.2) WILD-TYPE 255  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED    118    9
  DEL PEAK 10(4P16.2) WILD-TYPE  255   46
                               clus
vv                              DEL PEAK 10(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                  118
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK 10(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    255
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED     3 125
  DEL PEAK 10(4P16.2) WILD-TYPE   0 302
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED      3  125
  DEL PEAK 10(4P16.2) WILD-TYPE    0  302
     clus
vv    DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  NO                            3                             0
  YES                         125                           302
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4P16.2) MUTATED    89   0  13   5
  DEL PEAK 10(4P16.2) WILD-TYPE 216   3  11  19
D33V10, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  R0                          89                           216
  R1                           0                             3
  R2                          13                            11
  RX                           5                            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"
D33V11, 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                          11    61
  DEL PEAK 10(4P16.2) WILD-TYPE                        30   150
D33V12, multiclass
                                  clus
vv                                 DEL PEAK 10(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     61
                                  clus
vv                                 DEL PEAK 10(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   30
  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(34) Variable = DEL PEAK 11(4Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q22.1) MUTATED   101  33
  DEL PEAK 11(4Q22.1) WILD-TYPE 228  51
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          134                           279 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                           33                            51 
$`DEL PEAK 11(4Q22.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       37.05        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       29.16        24.16        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 
       52.44         9.63         5.03         1.02        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 
       38.99        37.05        34.03        29.00        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       13.02        19.99         6.05         2.01        50.04        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00         0.99         0.99        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       17.03         0.99        33.07         0.99        31.07        17.03 
TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        2.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q 
       50.99        26.01        24.00        27.02        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       17.03        15.02        32.02        26.01         2.96        39.98 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       41.00         1.58         1.02         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
        0.95         0.20         5.52         5.13        83.80        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       12.10        29.56         2.14         3.29         1.35       102.44 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       48.20         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       11.01        13.05        11.08        11.01        14.99        13.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 
       20.19        17.75         1.32         7.92        15.12        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D8 
        9.04        13.41        12.00        11.38        24.43        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6460 
        7.50        44.32         6.12        14.04        35.97        13.38 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       16.24        33.67        35.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       23.51        45.11        36.72        91.79        46.75         4.11 
TCGA-NH-A6GA TCGA-QG-A5YV 
        5.98        26.99 

$`DEL PEAK 11(4Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.25        16.04        14.53        32.91        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        8.05        19.07        19.07        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-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-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-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-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       15.95        14.93        36.03        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-3971 TCGA-AA-3973 
       24.00        33.01        26.01        24.00        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01        27.02         0.99        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07         0.26         0.33         0.10 
TCGA-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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       37.02         8.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       16.01        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       21.99        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       10.06        12.03        12.26        19.59        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        17.85         4.50        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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.64         1.51        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        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-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        1.28         0.53        19.43       107.67        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80         5.06         2.79 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        17.29        14.76 

  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                         0.20                          0.07 
  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 
                        20.09                         19.99 
[1] "0.2 - 102.4 (20.1)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.5"
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q22.1) MUTATED        13        0        8        36         2
  DEL PEAK 11(4Q22.1) WILD-TYPE      59        1       20        91         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q22.1) MUTATED           0         3          8         21
  DEL PEAK 11(4Q22.1) WILD-TYPE         1        18          5         32
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q22.1) MUTATED           18       20         4         1
  DEL PEAK 11(4Q22.1) WILD-TYPE         20       22        12         0
D34V3, multiclass
            clus
vv           DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  STAGE I                             13                            59
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           36                            91
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           8                             5
  STAGE IIIB                          21                            32
  STAGE IIIC                          18                            20
  STAGE IV                            20                            22
  STAGE IVA                            4                            12
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 11(4Q22.1) MUTATED       4  17  99  18
  DEL PEAK 11(4Q22.1) WILD-TYPE     7  59 195  30
D34V4, multiclass
       clus
vv      DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  T0+T1                           4                             7
  T2                             17                            59
  T3                             99                           195
  T4                             18                            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 11(4Q22.1) MUTATED    63  43  32
  DEL PEAK 11(4Q22.1) WILD-TYPE 189  58  44
D34V5, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  N0                          63                           189
  N1                          43                            58
  N2                          32                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 11(4Q22.1) MUTATED    93  21   3   1  16
  DEL PEAK 11(4Q22.1) WILD-TYPE 227  29   4   0  29
D34V6, multiclass
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  M0                           93                           227
  M1                           21                            29
  M1A                           3                             4
  M1B                           1                             0
  MX                           16                            29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    62  76
  DEL PEAK 11(4Q22.1) WILD-TYPE 141 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     62   76
  DEL PEAK 11(4Q22.1) WILD-TYPE  141  151
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  FEMALE                          62                           141
  MALE                            76                           151
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED   128   9
  DEL PEAK 11(4Q22.1) WILD-TYPE 245  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED    128    9
  DEL PEAK 11(4Q22.1) WILD-TYPE  245   46
                               clus
vv                              DEL PEAK 11(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                  128
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK 11(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    245
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED     3 135
  DEL PEAK 11(4Q22.1) WILD-TYPE   0 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED      3  135
  DEL PEAK 11(4Q22.1) WILD-TYPE    0  292
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  NO                            3                             0
  YES                         135                           292
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q22.1) MUTATED    98   1   9   7
  DEL PEAK 11(4Q22.1) WILD-TYPE 207   2  15  17
D34V10, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  R0                          98                           207
  R1                           1                             2
  R2                           9                            15
  RX                           7                            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"
D34V11, 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                          15    70
  DEL PEAK 11(4Q22.1) WILD-TYPE                        26   141
D34V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     70
                                  clus
vv                                 DEL PEAK 11(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   26
  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(35) Variable = DEL PEAK 12(4Q35.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q35.1) MUTATED   112  30
  DEL PEAK 12(4Q35.1) WILD-TYPE 217  54
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          142                           271 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                           30                            54 
$`DEL PEAK 12(4Q35.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 
       37.05        37.25        34.65        32.45        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       24.13        25.08        24.16        20.61        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       20.28        61.84        52.44         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 
       38.99        37.05        34.03        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       33.99        21.01        13.02        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       54.02         2.01        50.04        37.05        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
        0.99        38.99        36.95        37.02        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 
       33.07        36.03         0.99        31.07        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       26.01        24.00         7.96        34.03        17.03        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01X 
       15.02        32.02        31.00        35.01         1.02        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
        2.96        39.98         2.01        41.00         1.02         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 
       14.50        16.31         0.95         5.52        75.25         5.65 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5256 
        5.13        65.00        12.10        29.56         2.24         2.14 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        0.10         1.35        48.20         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.03        30.08         5.03        15.02        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       14.04        29.03        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       11.01        14.99        13.51        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 
        7.92        17.85         7.53         9.04        13.41        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 
      140.38         7.50        44.32       131.51         6.12        14.04 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
       26.47        13.38         1.55        16.24        33.67        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
        8.35        82.39        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75         4.11         5.98        26.99 

$`DEL PEAK 12(4Q35.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       44.91        16.04        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       27.09        22.52         8.38        25.18        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        19.07        29.00        12.99         0.99 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       13.94        61.02         6.97        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-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3858 
        1.02        17.98        15.95        14.93        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       13.05        34.06        25.02        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         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         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       50.37        58.39         1.41        32.94        83.80        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       62.79        61.41        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19         1.94         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.26         0.33        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 
       26.04        27.02        22.98        16.01        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       19.59        11.51        20.42        18.25        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        49.91        12.59       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       35.87        16.31        29.59         1.28         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      107.67        28.21        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        51.75        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX 
       47.15        52.80         5.06         2.79         5.59        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                         0.10                          0.07 
  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 
                       20.795                        19.430 
[1] "0.1 - 140.4 (20.8)" "0.1 - 139.2 (19.4)"
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(4Q35.1) MUTATED        16        0        7        41         1
  DEL PEAK 12(4Q35.1) WILD-TYPE      56        1       21        86         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q35.1) MUTATED           0         7          7         19
  DEL PEAK 12(4Q35.1) WILD-TYPE         1        14          6         34
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(4Q35.1) MUTATED           17       22         6         0
  DEL PEAK 12(4Q35.1) WILD-TYPE         21       20        10         1
D35V3, multiclass
            clus
vv           DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  STAGE I                             16                            56
  STAGE IA                             0                             1
  STAGE II                             7                            21
  STAGE IIA                           41                            86
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            7                            14
  STAGE IIIA                           7                             6
  STAGE IIIB                          19                            34
  STAGE IIIC                          17                            21
  STAGE IV                            22                            20
  STAGE IVA                            6                            10
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 12(4Q35.1) MUTATED       4  20 104  18
  DEL PEAK 12(4Q35.1) WILD-TYPE     7  56 190  30
D35V4, multiclass
       clus
vv      DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  T0+T1                           4                             7
  T2                             20                            56
  T3                            104                           190
  T4                             18                            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    70  42  34
  DEL PEAK 12(4Q35.1) WILD-TYPE 182  59  42
D35V5, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  N0                          70                           182
  N1                          42                            59
  N2                          34                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 12(4Q35.1) MUTATED   102  24   4   0  15
  DEL PEAK 12(4Q35.1) WILD-TYPE 218  26   3   1  30
D35V6, multiclass
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  M0                          102                           218
  M1                           24                            26
  M1A                           4                             3
  M1B                           0                             1
  MX                           15                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED    75  71
  DEL PEAK 12(4Q35.1) WILD-TYPE 128 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED     75   71
  DEL PEAK 12(4Q35.1) WILD-TYPE  128  156
        clus
vv       DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  FEMALE                          75                           128
  MALE                            71                           156
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   133  12
  DEL PEAK 12(4Q35.1) WILD-TYPE 240  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    133   12
  DEL PEAK 12(4Q35.1) WILD-TYPE  240   43
                               clus
vv                              DEL PEAK 12(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                  133
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              DEL PEAK 12(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    240
  COLON MUCINOUS ADENOCARCINOMA                            43
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED     3 143
  DEL PEAK 12(4Q35.1) WILD-TYPE   0 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED      3  143
  DEL PEAK 12(4Q35.1) WILD-TYPE    0  284
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  NO                            3                             0
  YES                         143                           284
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q35.1) MUTATED   100   1  12   8
  DEL PEAK 12(4Q35.1) WILD-TYPE 205   2  12  16
D35V10, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  R0                         100                           205
  R1                           1                             2
  R2                          12                            12
  RX                           8                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, 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                          16    68
  DEL PEAK 12(4Q35.1) WILD-TYPE                        25   143
D35V12, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK 12(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   25
  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(36) Variable = DEL PEAK 13(5Q11.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q11.2) MUTATED    70  24
  DEL PEAK 13(5Q11.2) WILD-TYPE 259  60
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           94                           319 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           24                            60 
$`DEL PEAK 13(5Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        43.43        23.38        13.94        15.52 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 
       16.04        34.65        36.53        14.53        30.44        29.19 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3502 TCGA-AA-3538 TCGA-AA-3542 
       23.87         9.63         5.03        35.01        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       13.02        24.00        19.99        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 
       19.00        85.05         0.99        36.95        37.02        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3966 
        0.99        31.07        31.07        24.03         2.01         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       21.99        34.03        27.02        42.02         0.99        33.04 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        2.96         2.01        41.00         1.02         0.10         0.20 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31         0.20         5.65        65.00        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 
        5.23         1.94         3.29         1.35        48.20         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       14.04        29.03        13.02        17.75        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       10.13        12.43         9.04        44.32       131.51         6.12 
TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 
        8.61         1.55        33.67         8.35        82.39        45.11 
TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-QG-A5YV 
       36.00        91.79         4.11        26.99 

$`DEL PEAK 13(5Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
        5.06        46.65        17.79        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.05        37.25        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 
       22.52        24.13         8.38        20.61        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        1.02         3.02         1.02        37.05         1.02        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-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-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-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-3679 
       54.02         2.01        14.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       15.95        38.99        14.93        17.03         0.99        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        17.03         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         1.58         0.76         0.43         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-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-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        21.01         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        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         4.50        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         1.28 
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        43.07        61.87        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-QG-A5YX 
       52.80         5.06         2.79         5.98         5.59        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                        22.01                         19.59 
[1] "0.1 - 131.5 (22.0)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1.5"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q11.2) MUTATED        14        0        4        18         1
  DEL PEAK 13(5Q11.2) WILD-TYPE      58        1       24       109         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q11.2) MUTATED           0         4          6         11
  DEL PEAK 13(5Q11.2) WILD-TYPE         1        17          7         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q11.2) MUTATED           15       12         7         0
  DEL PEAK 13(5Q11.2) WILD-TYPE         23       30         9         1
D36V3, multiclass
            clus
vv           DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  STAGE I                             14                            58
  STAGE IA                             0                             1
  STAGE II                             4                            24
  STAGE IIA                           18                           109
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             7
  STAGE IIIB                          11                            42
  STAGE IIIC                          15                            23
  STAGE IV                            12                            30
  STAGE IVA                            7                             9
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 13(5Q11.2) MUTATED       3  17  65  11
  DEL PEAK 13(5Q11.2) WILD-TYPE     8  59 229  37
D36V4, multiclass
       clus
vv      DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  T0+T1                           3                             8
  T2                             17                            59
  T3                             65                           229
  T4                             11                            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 13(5Q11.2) MUTATED    43  27  26
  DEL PEAK 13(5Q11.2) WILD-TYPE 209  74  50
D36V5, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  N0                          43                           209
  N1                          27                            74
  N2                          26                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 13(5Q11.2) MUTATED    63  15   4   0  13
  DEL PEAK 13(5Q11.2) WILD-TYPE 257  35   3   1  32
D36V6, multiclass
     clus
vv    DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  M0                           63                           257
  M1                           15                            35
  M1A                           4                             3
  M1B                           0                             1
  MX                           13                            32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED    40  56
  DEL PEAK 13(5Q11.2) WILD-TYPE 163 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED     40   56
  DEL PEAK 13(5Q11.2) WILD-TYPE  163  171
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  FEMALE                          40                           163
  MALE                            56                           171
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED    90   6
  DEL PEAK 13(5Q11.2) WILD-TYPE 283  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED     90    6
  DEL PEAK 13(5Q11.2) WILD-TYPE  283   49
                               clus
vv                              DEL PEAK 13(5Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   90
  COLON MUCINOUS ADENOCARCINOMA                           6
                               clus
vv                              DEL PEAK 13(5Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    283
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED     3  93
  DEL PEAK 13(5Q11.2) WILD-TYPE   0 334
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED      3   93
  DEL PEAK 13(5Q11.2) WILD-TYPE    0  334
     clus
vv    DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  NO                            3                             0
  YES                          93                           334
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q11.2) MUTATED    63   1   6   4
  DEL PEAK 13(5Q11.2) WILD-TYPE 242   2  18  20
D36V10, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  R0                          63                           242
  R1                           1                             2
  R2                           6                            18
  RX                           4                            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"
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q11.2) MUTATED                                  1     2
  DEL PEAK 13(5Q11.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q11.2) MUTATED                           8    53
  DEL PEAK 13(5Q11.2) WILD-TYPE                        33   158
D36V12, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK 13(5Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   33
  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(37) Variable = DEL PEAK 14(5Q21.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q21.3) MUTATED    88  29
  DEL PEAK 14(5Q21.3) WILD-TYPE 241  55
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                          117                           296 
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                           29                            55 
$`DEL PEAK 14(5Q21.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       37.02        43.76        13.94        15.52        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 
       36.53        14.53        30.44        29.19        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU 
       25.08        25.18        24.16        21.76        23.87         9.63 
TCGA-AA-3488 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
        5.03         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-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 
       15.02        11.01        19.00        85.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       37.02         0.99        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3994 
       17.03        24.03        24.00         2.01        21.99        27.02 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T 
       34.03        27.02        42.02        15.02         0.99        33.04 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01         5.03        41.00         1.02         0.10 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4614 
        0.20         0.46        16.31         0.20        21.44         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        48.20         8.02        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-6172 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6530 
       29.03        13.02        11.01        11.08        19.59        20.42 
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-A288 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 
       14.04        26.47       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-QG-A5YV 
       91.79         4.11        26.99 

$`DEL PEAK 14(5Q21.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 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-A6-6141 TCGA-A6-6650 TCGA-A6-6652 
       32.71        29.16        22.52         8.38        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 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        52.44         1.02         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01         0.92        47.05         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 
       14.93        17.03        36.03        32.05        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       17.03        14.99        21.99        34.98        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-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-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        1.58         0.76         0.43         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.95        15.75        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       50.37        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 
        2.01       124.27        23.05        20.02        37.02        27.02 
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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       15.02        14.04        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 
       20.19        17.75        18.25         1.32         7.92         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59         7.50       131.51       135.65       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
      119.93        35.97        60.79        95.18        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       55.04        51.75        39.42        35.93        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         5.06         2.79         5.98         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE 
                        19.59                         20.07 
[1] "0.1 - 140.4 (19.6)" "0.1 - 139.2 (20.1)"
[1] "hr=" "1.4"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q21.3) MUTATED        15        0        5        26         0
  DEL PEAK 14(5Q21.3) WILD-TYPE      57        1       23       101         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q21.3) MUTATED           0         5          8         16
  DEL PEAK 14(5Q21.3) WILD-TYPE         1        16          5         37
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q21.3) MUTATED           17       17         8         0
  DEL PEAK 14(5Q21.3) WILD-TYPE         21       25         8         1
D37V3, multiclass
            clus
vv           DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  STAGE I                             15                            57
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           26                           101
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           8                             5
  STAGE IIIB                          16                            37
  STAGE IIIC                          17                            21
  STAGE IV                            17                            25
  STAGE IVA                            8                             8
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 14(5Q21.3) MUTATED       3  19  85  14
  DEL PEAK 14(5Q21.3) WILD-TYPE     8  57 209  34
D37V4, multiclass
       clus
vv      DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  T0+T1                           3                             8
  T2                             19                            57
  T3                             85                           209
  T4                             14                            34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 14(5Q21.3) MUTATED    52  36  33
  DEL PEAK 14(5Q21.3) WILD-TYPE 200  65  43
D37V5, multiclass
    clus
vv   DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  N0                          52                           200
  N1                          36                            65
  N2                          33                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 14(5Q21.3) MUTATED    81  20   5   0  13
  DEL PEAK 14(5Q21.3) WILD-TYPE 239  30   2   1  32
D37V6, multiclass
     clus
vv    DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  M0                           81                           239
  M1                           20                            30
  M1A                           5                             2
  M1B                           0                             1
  MX                           13                            32
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.3) MUTATED    54  67
  DEL PEAK 14(5Q21.3) WILD-TYPE 149 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.3) MUTATED     54   67
  DEL PEAK 14(5Q21.3) WILD-TYPE  149  160
        clus
vv       DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  FEMALE                          54                           149
  MALE                            67                           160
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.3) MUTATED   110  11
  DEL PEAK 14(5Q21.3) WILD-TYPE 263  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.3) MUTATED    110   11
  DEL PEAK 14(5Q21.3) WILD-TYPE  263   44
                               clus
vv                              DEL PEAK 14(5Q21.3) MUTATED
  COLON ADENOCARCINOMA                                  110
  COLON MUCINOUS ADENOCARCINOMA                          11
                               clus
vv                              DEL PEAK 14(5Q21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    263
  COLON MUCINOUS ADENOCARCINOMA                            44
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.3) MUTATED     3 118
  DEL PEAK 14(5Q21.3) WILD-TYPE   0 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.3) MUTATED      3  118
  DEL PEAK 14(5Q21.3) WILD-TYPE    0  309
     clus
vv    DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  NO                            3                             0
  YES                         118                           309
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q21.3) MUTATED    77   1  10   5
  DEL PEAK 14(5Q21.3) WILD-TYPE 228   2  14  19
D37V10, multiclass
    clus
vv   DEL PEAK 14(5Q21.3) MUTATED DEL PEAK 14(5Q21.3) WILD-TYPE
  R0                          77                           228
  R1                           1                             2
  R2                          10                            14
  RX                           5                            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"
D37V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q21.3) MUTATED                                  1     2
  DEL PEAK 14(5Q21.3) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q21.3) MUTATED                           7    68
  DEL PEAK 14(5Q21.3) WILD-TYPE                        34   143
D37V12, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK 14(5Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   34
  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 15(5Q23.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q23.1) MUTATED    81  27
  DEL PEAK 15(5Q23.1) WILD-TYPE 248  57
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                          108                           305 
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                           27                            57 
$`DEL PEAK 15(5Q23.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       37.02        43.76        13.94        16.04        36.53        14.53 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       30.44        29.19        27.09        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       24.16        21.76        23.87         9.63         5.03         1.02 
TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 
        1.02        37.05        26.01        12.99        13.02        24.00 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3688 TCGA-AA-3697 
       19.99        61.02        50.04        47.01        19.00        85.05 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
        0.99        36.95        37.02         0.99        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       31.07        17.03        24.03        24.00         2.01        21.99 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T 
       34.03        27.02        42.02        15.02         0.99        33.04 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01         5.03        41.00         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4614 
        0.76         0.20        16.31         0.20        21.44         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-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6751 TCGA-CM-4747 
        1.94         3.29         1.35        48.20       124.27         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       26.04         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        13.02        11.08        19.59        15.12 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       17.85        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28G TCGA-DM-A28H 
      140.38        44.32         6.12        26.47        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 
       98.24         8.61        13.38         1.55        33.67         8.35 
TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-QG-A5YV 
       82.39        45.11        36.00        91.79         4.11        26.99 

$`DEL PEAK 15(5Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        33.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        13.94        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        14.93        17.03 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       36.03        32.05        31.07        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-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       17.03        14.99        21.99        34.98        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-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-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        1.58         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.95        15.75        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       50.37        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       61.41        49.41        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.01         2.93         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       23.05        20.02        37.02        27.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       12.00        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32         7.92 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-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-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        46.75        47.15        52.80         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        17.29        14.76 

  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE 
                        19.79                         20.02 
[1] "0.1 - 140.4 (19.8)" "0.1 - 139.2 (20.0)"
[1] "hr=" "1.3"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(5Q23.1) MUTATED        15        0        6        25         0
  DEL PEAK 15(5Q23.1) WILD-TYPE      57        1       22       102         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q23.1) MUTATED           0         4          7         13
  DEL PEAK 15(5Q23.1) WILD-TYPE         1        17          6         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(5Q23.1) MUTATED           15       15         7         0
  DEL PEAK 15(5Q23.1) WILD-TYPE         23       27         9         1
D38V3, multiclass
            clus
vv           DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  STAGE I                             15                            57
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           25                           102
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           7                             6
  STAGE IIIB                          13                            40
  STAGE IIIC                          15                            23
  STAGE IV                            15                            27
  STAGE IVA                            7                             9
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 15(5Q23.1) MUTATED       3  18  79  12
  DEL PEAK 15(5Q23.1) WILD-TYPE     8  58 215  36
D38V4, multiclass
       clus
vv      DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  T0+T1                           3                             8
  T2                             18                            58
  T3                             79                           215
  T4                             12                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 15(5Q23.1) MUTATED    52  32  28
  DEL PEAK 15(5Q23.1) WILD-TYPE 200  69  48
D38V5, multiclass
    clus
vv   DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  N0                          52                           200
  N1                          32                            69
  N2                          28                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 15(5Q23.1) MUTATED    72  17   5   0  15
  DEL PEAK 15(5Q23.1) WILD-TYPE 248  33   2   1  30
D38V6, multiclass
     clus
vv    DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  M0                           72                           248
  M1                           17                            33
  M1A                           5                             2
  M1B                           0                             1
  MX                           15                            30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.1) MUTATED    47  65
  DEL PEAK 15(5Q23.1) WILD-TYPE 156 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.1) MUTATED     47   65
  DEL PEAK 15(5Q23.1) WILD-TYPE  156  162
        clus
vv       DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  FEMALE                          47                           156
  MALE                            65                           162
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.1) MUTATED   103   9
  DEL PEAK 15(5Q23.1) WILD-TYPE 270  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.1) MUTATED    103    9
  DEL PEAK 15(5Q23.1) WILD-TYPE  270   46
                               clus
vv                              DEL PEAK 15(5Q23.1) MUTATED
  COLON ADENOCARCINOMA                                  103
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK 15(5Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    270
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.1) MUTATED     3 109
  DEL PEAK 15(5Q23.1) WILD-TYPE   0 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.1) MUTATED      3  109
  DEL PEAK 15(5Q23.1) WILD-TYPE    0  318
     clus
vv    DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  NO                            3                             0
  YES                         109                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q23.1) MUTATED    68   1   9   6
  DEL PEAK 15(5Q23.1) WILD-TYPE 237   2  15  18
D38V10, multiclass
    clus
vv   DEL PEAK 15(5Q23.1) MUTATED DEL PEAK 15(5Q23.1) WILD-TYPE
  R0                          68                           237
  R1                           1                             2
  R2                           9                            15
  RX                           6                            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"
D38V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(5Q23.1) MUTATED                                  1     2
  DEL PEAK 15(5Q23.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q23.1) MUTATED                           7    63
  DEL PEAK 15(5Q23.1) WILD-TYPE                        34   148
D38V12, multiclass
                                  clus
vv                                 DEL PEAK 15(5Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 15(5Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   34
  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(39) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    40  13
  DEL PEAK 16(6P25.3) WILD-TYPE 289  71
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           53                           360 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           13                            71 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       37.02        15.52        16.04        25.18        24.16        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
       36.00         0.99        38.99        36.95        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 
       29.98        18.05        12.99        24.00         2.01        13.94 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O 
       30.02        18.05        27.02        38.07        26.01         0.92 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
        0.72         1.58         0.76         0.43         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
        2.24         3.06         2.14        29.06        22.98        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       11.01        14.99        20.19        17.75        17.85         7.53 
TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6317 
       13.32        26.47       117.07        33.67        36.00 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       42.28        44.91        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       20.98        19.99        19.99        78.08         6.05        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       33.07        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        17.03         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
        0.99        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         1.02         0.10         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.94         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 
       26.04         8.02        27.02        13.02        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5540 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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97        60.79        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-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.43                          0.07 
  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 
                        17.85                         20.27 
[1] "0.4 - 117.1 (17.9)" "0.1 - 140.4 (20.3)"
[1] "hr=" "1.6"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6P25.3) MUTATED         7        0        6        16         1
  DEL PEAK 16(6P25.3) WILD-TYPE      65        1       22       111         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED           0         3          2          3
  DEL PEAK 16(6P25.3) WILD-TYPE         1        18         11         50
                               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         33       37        12         1
D39V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              7                            65
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           16                           111
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           2                            11
  STAGE IIIB                           3                            50
  STAGE IIIC                           5                            33
  STAGE IV                             5                            37
  STAGE IVA                            4                            12
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 16(6P25.3) MUTATED       2   7  36   9
  DEL PEAK 16(6P25.3) WILD-TYPE     9  69 258  39
D39V4, multiclass
       clus
vv      DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T0+T1                           2                             9
  T2                              7                            69
  T3                             36                           258
  T4                              9                            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 16(6P25.3) MUTATED    33  11  10
  DEL PEAK 16(6P25.3) WILD-TYPE 219  90  66
D39V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          33                           219
  N1                          11                            90
  N2                          10                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 16(6P25.3) MUTATED    37   6   3   0   7
  DEL PEAK 16(6P25.3) WILD-TYPE 283  44   4   1  38
D39V6, multiclass
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  M0                           37                           283
  M1                            6                            44
  M1A                           3                             4
  M1B                           0                             1
  MX                            7                            38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    19  35
  DEL PEAK 16(6P25.3) WILD-TYPE 184 192
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     19   35
  DEL PEAK 16(6P25.3) WILD-TYPE  184  192
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          19                           184
  MALE                            35                           192
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    49   5
  DEL PEAK 16(6P25.3) WILD-TYPE 324  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     49    5
  DEL PEAK 16(6P25.3) WILD-TYPE  324   50
                               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                                    324
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     0  54
  DEL PEAK 16(6P25.3) WILD-TYPE   3 373
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      0   54
  DEL PEAK 16(6P25.3) WILD-TYPE    3  373
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                            0                             3
  YES                          54                           373
[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 268   3  23  19
D39V10, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          37                           268
  R1                           0                             3
  R2                           1                            23
  RX                           5                            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"
D39V11, 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                        40   185
D39V12, 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                                   40
  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(40) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D40V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    41  17
  DEL PEAK 17(6Q26) WILD-TYPE 288  67
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         58                         355 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         17                          67 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6649 
       37.02        42.28        45.60        32.45        22.52        24.16 
TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       20.28         5.03        13.02        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3837 
       11.01        37.05        36.00        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        36.03        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        2.01        18.05        17.03         0.99        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         1.58         0.43         0.46        16.31 
TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        0.20         5.13        49.41         3.19         2.24         3.06 
TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
        2.14        11.01        13.05        11.08        11.01        14.99 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-DM-A1HA 
       20.19        17.75        15.12         7.53        13.32       131.51 
TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA 
        1.55        33.67        82.39         5.98 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       19.00         5.03        26.99        19.04         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-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        17.03         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         1.02         0.10         0.76         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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-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-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        5.23        11.74         1.94         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-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-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       13.02        15.02        14.04        12.95        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-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 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-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11         5.06         2.79         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       0.20                        0.07 
  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 
                     15.715                      20.980 
[1] "0.2 - 131.5 (15.7)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.8"
D40V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(6Q26) MUTATED         8        0        6        10         1
  DEL PEAK 17(6Q26) WILD-TYPE      64        1       22       117         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           0         4          1          8
  DEL PEAK 17(6Q26) WILD-TYPE         1        17         12         45
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(6Q26) MUTATED            9        9         3         1
  DEL PEAK 17(6Q26) WILD-TYPE         29       33        13         0
D40V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            8                          64
  STAGE IA                           0                           1
  STAGE II                           6                          22
  STAGE IIA                         10                         117
  STAGE IIB                          1                           7
  STAGE IIC                          0                           1
  STAGE III                          4                          17
  STAGE IIIA                         1                          12
  STAGE IIIB                         8                          45
  STAGE IIIC                         9                          29
  STAGE IV                           9                          33
  STAGE IVA                          3                          13
  STAGE IVB                          1                           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                          T0+T1  T2  T3  T4
  DEL PEAK 17(6Q26) MUTATED       2   7  42   9
  DEL PEAK 17(6Q26) WILD-TYPE     9  69 252  39
D40V4, multiclass
       clus
vv      DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T0+T1                         2                           9
  T2                            7                          69
  T3                           42                         252
  T4                            9                          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 17(6Q26) MUTATED    27  14  19
  DEL PEAK 17(6Q26) WILD-TYPE 225  87  57
D40V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        27                         225
  N1                        14                          87
  N2                        19                          57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 17(6Q26) MUTATED    37  10   2   1   9
  DEL PEAK 17(6Q26) WILD-TYPE 283  40   5   0  36
D40V6, multiclass
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  M0                         37                         283
  M1                         10                          40
  M1A                         2                           5
  M1B                         1                           0
  MX                          9                          36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    27  33
  DEL PEAK 17(6Q26) WILD-TYPE 176 194
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     27   33
  DEL PEAK 17(6Q26) WILD-TYPE  176  194
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        27                         176
  MALE                          33                         194
[1] 2 2
[1] FALSE
D40V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    52   8
  DEL PEAK 17(6Q26) WILD-TYPE 321  47
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     52    8
  DEL PEAK 17(6Q26) WILD-TYPE  321   47
                               clus
vv                              DEL PEAK 17(6Q26) MUTATED
  COLON ADENOCARCINOMA                                 52
  COLON MUCINOUS ADENOCARCINOMA                         8
                               clus
vv                              DEL PEAK 17(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                  321
  COLON MUCINOUS ADENOCARCINOMA                          47
[1] 2 2
[1] FALSE
D40V9, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     0  60
  DEL PEAK 17(6Q26) WILD-TYPE   3 367
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      0   60
  DEL PEAK 17(6Q26) WILD-TYPE    3  367
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                          0                           3
  YES                        60                         367
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    39   1   5   6
  DEL PEAK 17(6Q26) WILD-TYPE 266   2  19  18
D40V10, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        39                         266
  R1                         1                           2
  R2                         5                          19
  RX                         6                          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"
D40V11, 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                           4    26
  DEL PEAK 17(6Q26) WILD-TYPE                        37   185
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 17(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   26
                                  clus
vv                                 DEL PEAK 17(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 37
  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(41) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(7Q31.1) MUTATED     9   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 320  82
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           11                           402 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                            2                            82 
$`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        17.03        35.01        21.37        14.50        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6932 TCGA-DM-A0XD 
       22.03         5.03        15.02        11.38        24.43 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-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         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        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         0.99        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 
        1.58         1.02         0.10         0.76         0.20         0.43 
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-AZ-4308 
        0.20        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-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-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        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-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-6169 
       29.03        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-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32         7.92        15.12        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        12.00        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         5.03                          0.07 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        35.01                        140.38 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        21.37                         19.99 
[1] "5.0 - 35.0 (21.4)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1.1"
D41V2, 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      70        1       28       122         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         12         52
                               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         37       42        15         1
D41V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              2                            70
  STAGE IA                             0                             1
  STAGE II                             0                            28
  STAGE IIA                            5                           122
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            12
  STAGE IIIB                           1                            52
  STAGE IIIC                           1                            37
  STAGE IV                             0                            42
  STAGE IVA                            1                            15
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 18(7Q31.1) MUTATED       0   3   9   0
  DEL PEAK 18(7Q31.1) WILD-TYPE    11  73 285  48
D41V4, multiclass
       clus
vv      DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T0+T1                           0                            11
  T2                              3                            73
  T3                              9                           285
  T4                              0                            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 18(7Q31.1) MUTATED     7   3   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 245  98  74
D41V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                           7                           245
  N1                           3                            98
  N2                           2                            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 18(7Q31.1) MUTATED    11   0   1   0   0
  DEL PEAK 18(7Q31.1) WILD-TYPE 309  50   6   1  45
D41V6, multiclass
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  M0                           11                           309
  M1                            0                            50
  M1A                           1                             6
  M1B                           0                             1
  MX                            0                            45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     7   5
  DEL PEAK 18(7Q31.1) WILD-TYPE 196 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      7    5
  DEL PEAK 18(7Q31.1) WILD-TYPE  196  222
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           7                           196
  MALE                             5                           222
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    11   1
  DEL PEAK 18(7Q31.1) WILD-TYPE 362  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     11    1
  DEL PEAK 18(7Q31.1) WILD-TYPE  362   54
                               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                                    362
  COLON MUCINOUS ADENOCARCINOMA                            54
[1] 2 2
[1] FALSE
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     0  12
  DEL PEAK 18(7Q31.1) WILD-TYPE   3 415
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      0   12
  DEL PEAK 18(7Q31.1) WILD-TYPE    3  415
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                            0                             3
  YES                          12                           415
[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 294   3  24  24
D41V10, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          11                           294
  R1                           0                             3
  R2                           0                            24
  RX                           0                            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"
D41V11, 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                        41   202
D41V12, 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                                   41
  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(42) Variable = DEL PEAK 19(8P23.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P23.3) MUTATED   138  36
  DEL PEAK 19(8P23.3) WILD-TYPE 191  48
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          174                           239 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                           36                            48 
$`DEL PEAK 19(8P23.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       31.63        29.19        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       58.03        38.99        24.03        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       23.01        19.99        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       36.00        85.05        37.02        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-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
        2.01         2.01        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       17.03        15.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
       37.02         2.96        39.98        41.00        40.96         4.21 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        1.58         1.02         0.20        16.31        15.75         0.20 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        5.52        75.25         5.65        83.80        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 TCGA-CM-4751 
        3.29         0.07         1.35        15.62        48.20        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       13.02        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 
       17.03        14.04        21.99        13.02        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       11.08        10.06        12.26        11.51        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
        7.92        15.12        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
      130.65        49.91        13.32       140.38       131.51         6.12 
TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 
       26.47        35.97        60.79       117.07        13.38        13.64 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
        1.55        16.31         0.53         8.35        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       61.87        44.68        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB 
       26.43        35.80        91.79         5.06         5.98         5.59 

$`DEL PEAK 19(8P23.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
        5.06        46.65        23.38        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       16.04        14.53        32.45        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 
       22.09        22.06        32.71        22.52         8.38        24.16 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02         3.02        35.01        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-3548 TCGA-AA-3554 TCGA-AA-3555 
       19.07        19.07        29.00        33.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       20.98        13.94        61.02         6.97        54.02         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       50.04        47.05        11.01         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
        0.99        32.05        53.00        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3968 
       24.00        33.01        26.01        24.00        20.98        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       50.99        13.05        25.02        19.07        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        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02         0.99        14.99        21.99        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H 
       35.01        35.01        26.01        39.06        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        5.03         0.92        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
       21.37        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.43         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       21.44        17.82         5.19        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        22.36        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 
      100.01         2.24         3.06         2.14         3.25         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       29.06        15.02        15.02        15.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 
       12.95        11.08        11.01        12.03        14.99        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 
       13.51        20.19        20.42        18.25        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       17.13        16.14        12.39        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 
        1.51        12.00        10.26       119.70        92.75        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       81.37       119.93        98.24        95.18         8.61        11.11 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18        35.87        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        1.28        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 
       43.07        53.62        55.04        51.75        45.11        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        26.17        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        4.11         2.79        26.99        17.29        14.76 

  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  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                         19.07 
[1] "0.1 - 140.4 (21.5)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1"  
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P23.3) MUTATED        24        0        8        41         2
  DEL PEAK 19(8P23.3) WILD-TYPE      48        1       20        86         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P23.3) MUTATED           0        10          6         25
  DEL PEAK 19(8P23.3) WILD-TYPE         1        11          7         28
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P23.3) MUTATED           23       27         8         1
  DEL PEAK 19(8P23.3) WILD-TYPE         15       15         8         0
D42V3, multiclass
            clus
vv           DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  STAGE I                             24                            48
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           41                            86
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                           10                            11
  STAGE IIIA                           6                             7
  STAGE IIIB                          25                            28
  STAGE IIIC                          23                            15
  STAGE IV                            27                            15
  STAGE IVA                            8                             8
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 19(8P23.3) MUTATED       1  30 128  19
  DEL PEAK 19(8P23.3) WILD-TYPE    10  46 166  29
D42V4, multiclass
       clus
vv      DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  T0+T1                           1                            10
  T2                             30                            46
  T3                            128                           166
  T4                             19                            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
  DEL PEAK 19(8P23.3) MUTATED    83  49  45
  DEL PEAK 19(8P23.3) WILD-TYPE 169  52  31
D42V5, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  N0                          83                           169
  N1                          49                            52
  N2                          45                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 19(8P23.3) MUTATED   123  31   4   1  17
  DEL PEAK 19(8P23.3) WILD-TYPE 197  19   3   0  28
D42V6, multiclass
     clus
vv    DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  M0                          123                           197
  M1                           31                            19
  M1A                           4                             3
  M1B                           1                             0
  MX                           17                            28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED    74 104
  DEL PEAK 19(8P23.3) WILD-TYPE 129 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED     74  104
  DEL PEAK 19(8P23.3) WILD-TYPE  129  123
        clus
vv       DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  FEMALE                          74                           129
  MALE                           104                           123
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED   161  16
  DEL PEAK 19(8P23.3) WILD-TYPE 212  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED    161   16
  DEL PEAK 19(8P23.3) WILD-TYPE  212   39
                               clus
vv                              DEL PEAK 19(8P23.3) MUTATED
  COLON ADENOCARCINOMA                                  161
  COLON MUCINOUS ADENOCARCINOMA                          16
                               clus
vv                              DEL PEAK 19(8P23.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    212
  COLON MUCINOUS ADENOCARCINOMA                            39
[1] 2 2
[1] FALSE
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED     2 176
  DEL PEAK 19(8P23.3) WILD-TYPE   1 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED      2  176
  DEL PEAK 19(8P23.3) WILD-TYPE    1  251
     clus
vv    DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  NO                            2                             1
  YES                         176                           251
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P23.3) MUTATED   120   1  14   6
  DEL PEAK 19(8P23.3) WILD-TYPE 185   2  10  18
D42V10, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  R0                         120                           185
  R1                           1                             2
  R2                          14                            10
  RX                           6                            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"
D42V11, 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                          19    88
  DEL PEAK 19(8P23.3) WILD-TYPE                        22   123
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 19(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     88
                                  clus
vv                                 DEL PEAK 19(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   22
  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(43) Variable = DEL PEAK 20(8P22) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(8P22) MUTATED   145  44
  DEL PEAK 20(8P22) WILD-TYPE 184  40
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        189                         224 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                         44                          40 
$`DEL PEAK 20(8P22) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 
       31.63        30.44        29.19        23.61        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       20.28        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 
       37.05         1.02        38.99        24.03        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        19.99        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        14.01        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 
        5.98        37.05        19.00        36.00        85.05        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        36.03         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3956 
       17.03        24.03        27.02        29.98         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       16.08        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        17.03        17.03        14.99        15.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       12.00        31.00         1.02        33.04        37.02         2.96 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 
        5.03        41.00        40.96         4.21         1.58         1.02 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
        0.20         0.46        16.31        15.75         0.20         5.52 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25         5.65        83.80        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07         1.35       102.44        15.62        48.20 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
        5.03        17.03        14.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        13.05        11.08        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        17.75         1.32         7.92        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F 
      140.38        44.32       131.51         6.12        26.47        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07         8.61        13.38        11.11        13.64 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
        1.55        16.31         1.28         0.53         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       74.56        61.87        44.68        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        35.80        91.79        46.75 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB 
        5.06         5.98         5.59 

$`DEL PEAK 20(8P22) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
        5.06        46.65        23.38        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       16.04        14.53        32.45        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       32.71        22.52         8.38        24.16        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         1.02         3.02 
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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       19.07        29.00         0.99        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       13.94        61.02         6.97         0.92        50.04        47.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 
       36.95        14.93        17.03        32.05        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98         2.01        21.99        50.99        13.05 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       38.07         1.02        35.01        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         2.01         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         0.43         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        32.94         5.13        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 
      100.01         2.24         3.06         2.14         3.25         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
        0.33         0.10        17.56        40.34        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.01         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         8.02        26.04         8.02        29.06 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       16.04        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       11.01        10.06        12.03        14.99        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 
       18.25        17.85         4.50        17.13        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
      119.70        92.75        12.59         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M 
      139.17        14.04        81.37       119.93        98.24        95.18 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18        35.87        29.59        16.24        33.67 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 
       35.41        19.43       107.67        28.21        82.39        43.07 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 
       53.62        55.04        51.75        45.11        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5YV 
       26.17        47.15        52.80         4.11         2.79        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                       0.07                        0.07 
  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 
                      21.01                       19.07 
[1] "0.1 - 140.4 (21.0)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.3"
D43V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8P22) MUTATED        24        0        9        42         2
  DEL PEAK 20(8P22) WILD-TYPE      48        1       19        85         6
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P22) MUTATED           0        10          8         28
  DEL PEAK 20(8P22) WILD-TYPE         1        11          5         25
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8P22) MUTATED           25       28        12         1
  DEL PEAK 20(8P22) WILD-TYPE         13       14         4         0
D43V3, multiclass
            clus
vv           DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  STAGE I                           24                          48
  STAGE IA                           0                           1
  STAGE II                           9                          19
  STAGE IIA                         42                          85
  STAGE IIB                          2                           6
  STAGE IIC                          0                           1
  STAGE III                         10                          11
  STAGE IIIA                         8                           5
  STAGE IIIB                        28                          25
  STAGE IIIC                        25                          13
  STAGE IV                          28                          14
  STAGE IVA                         12                           4
  STAGE IVB                          1                           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                          T0+T1  T2  T3  T4
  DEL PEAK 20(8P22) MUTATED       2  29 139  22
  DEL PEAK 20(8P22) WILD-TYPE     9  47 155  26
D43V4, multiclass
       clus
vv      DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  T0+T1                         2                           9
  T2                           29                          47
  T3                          139                         155
  T4                           22                          26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 20(8P22) MUTATED    87  53  51
  DEL PEAK 20(8P22) WILD-TYPE 165  48  25
D43V5, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  N0                        87                         165
  N1                        53                          48
  N2                        51                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 20(8P22) MUTATED   131  36   4   1  18
  DEL PEAK 20(8P22) WILD-TYPE 189  14   3   0  27
D43V6, multiclass
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  M0                        131                         189
  M1                         36                          14
  M1A                         4                           3
  M1B                         1                           0
  MX                         18                          27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED    82 110
  DEL PEAK 20(8P22) WILD-TYPE 121 117
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED     82  110
  DEL PEAK 20(8P22) WILD-TYPE  121  117
        clus
vv       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  FEMALE                        82                         121
  MALE                         110                         117
[1] 2 2
[1] FALSE
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   175  16
  DEL PEAK 20(8P22) WILD-TYPE 198  39
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    175   16
  DEL PEAK 20(8P22) WILD-TYPE  198   39
                               clus
vv                              DEL PEAK 20(8P22) MUTATED
  COLON ADENOCARCINOMA                                175
  COLON MUCINOUS ADENOCARCINOMA                        16
                               clus
vv                              DEL PEAK 20(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                  198
  COLON MUCINOUS ADENOCARCINOMA                          39
[1] 2 2
[1] FALSE
D43V9, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED     2 190
  DEL PEAK 20(8P22) WILD-TYPE   1 237
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED      2  190
  DEL PEAK 20(8P22) WILD-TYPE    1  237
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  NO                          2                           1
  YES                       190                         237
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(8P22) MUTATED   132   1  15   6
  DEL PEAK 20(8P22) WILD-TYPE 173   2   9  18
D43V10, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  R0                       132                         173
  R1                         1                           2
  R2                        15                           9
  RX                         6                          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"
D43V11, 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                          19   101
  DEL PEAK 20(8P22) WILD-TYPE                        22   110
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 20(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               19
  WHITE                                                  101
                                  clus
vv                                 DEL PEAK 20(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 22
  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(44) Variable = DEL PEAK 21(8P11.21) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(8P11.21) MUTATED    32  12
  DEL PEAK 21(8P11.21) WILD-TYPE 297  72
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                            44                            369 
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                            12                             72 
$`DEL PEAK 21(8P11.21) MUTATED`
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 TCGA-A6-6654 
       42.28        44.91        15.52        36.53        20.61        23.87 
TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3666 TCGA-AA-3842 TCGA-AA-3851 
        5.03        38.99        34.03         2.01        37.02        33.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3956 TCGA-AA-3976 TCGA-AA-3989 
       31.07        17.03        27.02        34.03        26.01         7.96 
TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02E TCGA-AA-A02F TCGA-AD-6965 TCGA-AY-6196 
        0.99        31.00         2.96        39.98         0.20         0.20 
TCGA-AY-A69D TCGA-AZ-4684 TCGA-CA-5797 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5538 
        5.52        65.00         3.29        17.03        13.05        12.26 
TCGA-D5-5540 TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A 
       13.51        17.75        49.91       140.38       131.51        26.47 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 
       35.97        13.38         1.55        23.51        61.87        35.93 
TCGA-G4-6317 TCGA-G4-6625 
       36.00        91.79 

$`DEL PEAK 21(8P11.21) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       17.79        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-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-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       15.02        11.01         5.98        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        36.95        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        20.98         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-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        39.06        51.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        1.58         1.02         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
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-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        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-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.03        14.99        19.59        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
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-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        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         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        74.56        43.07        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        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-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE 
                         26.24                          19.43 
[1] "0.2 - 140.4 (26.2)" "0.1 - 139.2 (19.4)"
[1] "hr=" "1.2"
D44V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(8P11.21) MUTATED         1        0        0        13         1
  DEL PEAK 21(8P11.21) WILD-TYPE      71        1       28       114         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8P11.21) MUTATED           0         1          2          7
  DEL PEAK 21(8P11.21) WILD-TYPE         1        20         11         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(8P11.21) MUTATED            8        8         2         1
  DEL PEAK 21(8P11.21) WILD-TYPE         30       34        14         0
D44V3, multiclass
            clus
vv           DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  STAGE I                               1                             71
  STAGE IA                              0                              1
  STAGE II                              0                             28
  STAGE IIA                            13                            114
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             1                             20
  STAGE IIIA                            2                             11
  STAGE IIIB                            7                             46
  STAGE IIIC                            8                             30
  STAGE IV                              8                             34
  STAGE IVA                             2                             14
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 21(8P11.21) MUTATED       0   3  37   5
  DEL PEAK 21(8P11.21) WILD-TYPE    11  73 257  43
D44V4, multiclass
       clus
vv      DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  T0+T1                            0                             11
  T2                               3                             73
  T3                              37                            257
  T4                               5                             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 21(8P11.21) MUTATED    16  14  15
  DEL PEAK 21(8P11.21) WILD-TYPE 236  87  61
D44V5, multiclass
    clus
vv   DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  N0                           16                            236
  N1                           14                             87
  N2                           15                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 21(8P11.21) MUTATED    28   9   1   1   4
  DEL PEAK 21(8P11.21) WILD-TYPE 292  41   6   0  41
D44V6, multiclass
     clus
vv    DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  M0                            28                            292
  M1                             9                             41
  M1A                            1                              6
  M1B                            1                              0
  MX                             4                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(8P11.21) MUTATED    22  23
  DEL PEAK 21(8P11.21) WILD-TYPE 181 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(8P11.21) MUTATED     22   23
  DEL PEAK 21(8P11.21) WILD-TYPE  181  204
        clus
vv       DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  FEMALE                           22                            181
  MALE                             23                            204
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(8P11.21) MUTATED    41   4
  DEL PEAK 21(8P11.21) WILD-TYPE 332  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(8P11.21) MUTATED     41    4
  DEL PEAK 21(8P11.21) WILD-TYPE  332   51
                               clus
vv                              DEL PEAK 21(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                    41
  COLON MUCINOUS ADENOCARCINOMA                            4
                               clus
vv                              DEL PEAK 21(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     332
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                               0   1
  DEL PEAK 21(8P11.21) MUTATED     1  44
  DEL PEAK 21(8P11.21) WILD-TYPE   2 383
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(8P11.21) MUTATED      1   44
  DEL PEAK 21(8P11.21) WILD-TYPE    2  383
     clus
vv    DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  NO                             1                              2
  YES                           44                            383
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(8P11.21) MUTATED    31   0   5   0
  DEL PEAK 21(8P11.21) WILD-TYPE 274   3  19  24
D44V10, multiclass
    clus
vv   DEL PEAK 21(8P11.21) MUTATED DEL PEAK 21(8P11.21) WILD-TYPE
  R0                           31                            274
  R1                            0                              3
  R2                            5                             19
  RX                            0                             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"
D44V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(8P11.21) MUTATED                                  1     1
  DEL PEAK 21(8P11.21) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P11.21) MUTATED                           4    22
  DEL PEAK 21(8P11.21) WILD-TYPE                        37   189
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 21(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 21(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    37
  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(45) Variable = DEL PEAK 22(9P21.3) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED    46   9
  DEL PEAK 22(9P21.3) WILD-TYPE 283  75
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           55                           358 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                            9                            75 
$`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 
        5.52         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         7.92 
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 
        5.98 

$`DEL PEAK 22(9P21.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        16.04        34.65        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
        1.02        35.01        63.98         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        13.02        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        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 
        1.58         1.02         0.10         0.76         0.43         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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41        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-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       29.56        11.74         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       11.51        20.42        17.75        18.25         1.32        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 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-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       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-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        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-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        26.99        17.29        14.76 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         0.20                          0.07 
  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 
                        16.31                         20.07 
[1] "0.2 - 85.0 (16.3)"  "0.1 - 140.4 (20.1)"
[1] "hr=" "1.1"
D45V2, 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      62        1       25       112         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         10         45
                               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         32       36        13         0
D45V3, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                             10                            62
  STAGE IA                             0                             1
  STAGE II                             3                            25
  STAGE IIA                           15                           112
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           3                            10
  STAGE IIIB                           8                            45
  STAGE IIIC                           6                            32
  STAGE IV                             6                            36
  STAGE IVA                            3                            13
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 22(9P21.3) MUTATED       2  13  35   9
  DEL PEAK 22(9P21.3) WILD-TYPE     9  63 259  39
D45V4, multiclass
       clus
vv      DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T0+T1                           2                             9
  T2                             13                            63
  T3                             35                           259
  T4                              9                            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 22(9P21.3) MUTATED    29  15  14
  DEL PEAK 22(9P21.3) WILD-TYPE 223  86  62
D45V5, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                          29                           223
  N1                          15                            86
  N2                          14                            62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 22(9P21.3) MUTATED    43   7   2   1   6
  DEL PEAK 22(9P21.3) WILD-TYPE 277  43   5   0  39
D45V6, multiclass
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  M0                           43                           277
  M1                            7                            43
  M1A                           2                             5
  M1B                           1                             0
  MX                            6                            39
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    23  36
  DEL PEAK 22(9P21.3) WILD-TYPE 180 191
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     23   36
  DEL PEAK 22(9P21.3) WILD-TYPE  180  191
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                          23                           180
  MALE                            36                           191
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    56   3
  DEL PEAK 22(9P21.3) WILD-TYPE 317  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     56    3
  DEL PEAK 22(9P21.3) WILD-TYPE  317   52
                               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                                    317
  COLON MUCINOUS ADENOCARCINOMA                            52
[1] 2 2
[1] FALSE
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     0  59
  DEL PEAK 22(9P21.3) WILD-TYPE   3 368
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      0   59
  DEL PEAK 22(9P21.3) WILD-TYPE    3  368
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                            0                             3
  YES                          59                           368
[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 264   2  21  21
D45V10, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                          41                           264
  R1                           1                             2
  R2                           3                            21
  RX                           3                            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"
D45V11, 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                        35   184
D45V12, 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                                   35
  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(46) Variable = DEL PEAK 23(10P15.3) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10P15.3) MUTATED    58  16
  DEL PEAK 23(10P15.3) WILD-TYPE 271  68
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            74                            339 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            16                             68 
$`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        17.79        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3673 
        1.02         6.97        13.02        19.99        54.02        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       37.05        36.00        85.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       24.03         2.01        50.99        24.00         7.96        34.03 
TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       18.05        42.02        21.99         0.99        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4323 
        1.02         0.43         0.46        14.50         0.20         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 
        5.65         5.13        65.00        62.79        29.56         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       11.08        17.75        15.12         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 
       13.41        82.39        61.87        55.04        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6626 
       26.04        46.75 

$`DEL PEAK 23(10P15.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        37.02        46.65        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5660 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-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       24.92        52.44         5.03         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
       13.94        61.02        78.08         6.05         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-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        17.03         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         1.58         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.76         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-AZ-4308 
       15.75        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
       50.37        58.39        32.94        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-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-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-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04        27.02        13.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02         5.03        17.03        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       28.21         8.35        23.51        74.56        43.07        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-G4-6625 TCGA-G4-6627 
       22.09        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                          0.20                           0.07 
  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 
                         20.99                          19.99 
[1] "0.2 - 85.0 (21.0)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1.1"
D46V2, 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      62        1       22       115         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10P15.3) MUTATED           1         2          4         10
  DEL PEAK 23(10P15.3) WILD-TYPE         0        19          9         43
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10P15.3) MUTATED            8       16         4         0
  DEL PEAK 23(10P15.3) WILD-TYPE         30       26        12         1
D46V3, multiclass
            clus
vv           DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  STAGE I                              10                             62
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            12                            115
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            4                              9
  STAGE IIIB                           10                             43
  STAGE IIIC                            8                             30
  STAGE IV                             16                             26
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 23(10P15.3) MUTATED       1  13  52   9
  DEL PEAK 23(10P15.3) WILD-TYPE    10  63 242  39
D46V4, multiclass
       clus
vv      DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  T0+T1                            1                             10
  T2                              13                             63
  T3                              52                            242
  T4                               9                             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 23(10P15.3) MUTATED    33  22  20
  DEL PEAK 23(10P15.3) WILD-TYPE 219  79  56
D46V5, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  N0                           33                            219
  N1                           22                             79
  N2                           20                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 23(10P15.3) MUTATED    47  19   1   0   7
  DEL PEAK 23(10P15.3) WILD-TYPE 273  31   6   1  38
D46V6, multiclass
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  M0                            47                            273
  M1                            19                             31
  M1A                            1                              6
  M1B                            0                              1
  MX                             7                             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    34  41
  DEL PEAK 23(10P15.3) WILD-TYPE 169 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     34   41
  DEL PEAK 23(10P15.3) WILD-TYPE  169  186
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  FEMALE                           34                            169
  MALE                             41                            186
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    68   7
  DEL PEAK 23(10P15.3) WILD-TYPE 305  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     68    7
  DEL PEAK 23(10P15.3) WILD-TYPE  305   48
                               clus
vv                              DEL PEAK 23(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                    68
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 23(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     305
  COLON MUCINOUS ADENOCARCINOMA                             48
[1] 2 2
[1] FALSE
D46V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED     2  73
  DEL PEAK 23(10P15.3) WILD-TYPE   1 354
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED      2   73
  DEL PEAK 23(10P15.3) WILD-TYPE    1  354
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  NO                             2                              1
  YES                           73                            354
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10P15.3) MUTATED    52   0   6   5
  DEL PEAK 23(10P15.3) WILD-TYPE 253   3  18  19
D46V10, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  R0                           52                            253
  R1                            0                              3
  R2                            6                             18
  RX                            5                             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"
D46V11, 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                           5    42
  DEL PEAK 23(10P15.3) WILD-TYPE                        36   169
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 23(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 23(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    36
  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(47) Variable = DEL PEAK 24(10Q21.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10Q21.1) MUTATED    68  20
  DEL PEAK 24(10Q21.1) WILD-TYPE 261  64
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            88                            325 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            20                             64 
$`DEL PEAK 24(10Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4107 
       37.02        17.79        35.11        45.60        34.65        32.45 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 
       30.44        32.71        29.16        22.52        25.18        20.61 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       23.87        61.84        52.44         9.63         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       38.99        33.99        21.01        13.02        19.99         6.05 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 
       50.04        37.05        36.00        85.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3989 
       17.03        24.03         2.01        21.99        50.99         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X TCGA-AA-A02F 
       34.03        42.02         0.99         1.02        26.01        39.98 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 
        5.03        41.00         0.79         1.02         0.43        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31         0.20         5.65        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 
        3.19         2.24         3.29         0.26         1.35         8.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 
       29.06        22.03         5.03        15.02        15.02        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6534 
       13.02        15.02        11.08        11.08        17.75         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       15.12        17.85         7.53         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 TCGA-G4-6307 TCGA-G4-6314 
       11.38        35.97       117.07        11.11        55.04        35.93 
TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 
       36.72        26.04        91.79        46.75 

$`DEL PEAK 24(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        46.65        43.76        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 
       19.66        20.28        16.24        24.92         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 
       29.00        26.01        12.99         0.99        14.01        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-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
        0.92        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 
       38.99        36.95        37.02        14.93        17.03        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-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        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-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         1.58         0.10         0.76         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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-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-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.07         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       13.02        22.98        30.08        16.01        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        13.05        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 
       11.51        20.19        20.42        18.25         1.32         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37       119.93        60.79        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       13.38        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        36.00        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                          0.20                           0.07 
  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 
                         20.30                          19.99 
[1] "0.2 - 117.1 (20.3)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q21.1) MUTATED        12        0        6        17         0
  DEL PEAK 24(10Q21.1) WILD-TYPE      60        1       22       110         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q21.1) MUTATED           1         2          3         12
  DEL PEAK 24(10Q21.1) WILD-TYPE         0        19         10         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q21.1) MUTATED           14       16         4         0
  DEL PEAK 24(10Q21.1) WILD-TYPE         24       26        12         1
D47V3, multiclass
            clus
vv           DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  STAGE I                              12                             60
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            17                            110
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            3                             10
  STAGE IIIB                           12                             41
  STAGE IIIC                           14                             24
  STAGE IV                             16                             26
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 24(10Q21.1) MUTATED       2  15  63  10
  DEL PEAK 24(10Q21.1) WILD-TYPE     9  61 231  38
D47V4, multiclass
       clus
vv      DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  T0+T1                            2                              9
  T2                              15                             61
  T3                              63                            231
  T4                              10                             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 24(10Q21.1) MUTATED    42  24  24
  DEL PEAK 24(10Q21.1) WILD-TYPE 210  77  52
D47V5, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  N0                           42                            210
  N1                           24                             77
  N2                           24                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 24(10Q21.1) MUTATED    61  18   2   0   8
  DEL PEAK 24(10Q21.1) WILD-TYPE 259  32   5   1  37
D47V6, multiclass
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  M0                            61                            259
  M1                            18                             32
  M1A                            2                              5
  M1B                            0                              1
  MX                             8                             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    43  47
  DEL PEAK 24(10Q21.1) WILD-TYPE 160 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     43   47
  DEL PEAK 24(10Q21.1) WILD-TYPE  160  180
        clus
vv       DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  FEMALE                           43                            160
  MALE                             47                            180
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    84   6
  DEL PEAK 24(10Q21.1) WILD-TYPE 289  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     84    6
  DEL PEAK 24(10Q21.1) WILD-TYPE  289   49
                               clus
vv                              DEL PEAK 24(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    84
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              DEL PEAK 24(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     289
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED     2  88
  DEL PEAK 24(10Q21.1) WILD-TYPE   1 339
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED      2   88
  DEL PEAK 24(10Q21.1) WILD-TYPE    1  339
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  NO                             2                              1
  YES                           88                            339
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10Q21.1) MUTATED    59   1  10   6
  DEL PEAK 24(10Q21.1) WILD-TYPE 246   2  14  18
D47V10, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  R0                           59                            246
  R1                            1                              2
  R2                           10                             14
  RX                            6                             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"
D47V11, 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                           8    48
  DEL PEAK 24(10Q21.1) WILD-TYPE                        33   163
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      48
                                  clus
vv                                 DEL PEAK 24(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    33
  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(48) Variable = DEL PEAK 25(10Q23.31) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(10Q23.31) MUTATED    80  20
  DEL PEAK 25(10Q23.31) WILD-TYPE 249  64
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            100                             313 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             20                              64 
$`DEL PEAK 25(10Q23.31) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        17.79        42.28        35.11        45.60        13.94 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       24.16        23.87        61.84         9.63         1.02         6.97 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 
        9.07        19.07        33.99        13.02        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 
        6.05        54.02        50.04        11.01        37.05        36.00 
TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       85.05        36.95        33.07        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       24.03         2.01        50.99         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 
        0.99        33.04        26.01        39.98        41.00         1.02 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
        0.43         0.46        14.50        16.31         5.19         5.52 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
        5.65        65.00        62.79        29.56         3.19         2.24 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       30.08         5.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 
       15.02        13.05        11.08        11.08        10.06        19.59 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       17.75        18.25         7.92        17.85        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.13         9.04        13.41       130.65        13.32       140.38 
TCGA-DM-A285 TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 
        6.12        11.11        16.24        33.67        55.04        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       36.00        26.04        13.78        46.75 

$`DEL PEAK 25(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        5.06        46.65        43.76        43.43        23.38        44.91 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
TCGA-A6-6650 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        52.44         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        34.03        29.00        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-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97         2.01        14.01         0.92        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-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
       17.03         0.99        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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-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         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        0.10         0.76         0.20         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 
       15.75         0.20        21.44        17.82        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.94         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        13.02        22.98        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-6678 
       14.99        12.99        14.04        11.01        12.95        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42         1.32        15.12         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       38.20        92.75        49.91        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-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-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        16.31        29.59         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        26.43        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                           0.26                            0.07 
  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 
                          18.66                           20.19 
[1] "0.3 - 140.4 (18.7)" "0.1 - 139.2 (20.2)"
[1] "hr=" "1"  
D48V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q23.31) MUTATED        14        1        6        22         0
  DEL PEAK 25(10Q23.31) WILD-TYPE      58        0       22       105         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q23.31) MUTATED           1         4          6         12
  DEL PEAK 25(10Q23.31) WILD-TYPE         0        17          7         41
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q23.31) MUTATED           11       17         5         1
  DEL PEAK 25(10Q23.31) WILD-TYPE         27       25        11         0
D48V3, multiclass
            clus
vv           DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  STAGE I                               14                              58
  STAGE IA                               1                               0
  STAGE II                               6                              22
  STAGE IIA                             22                             105
  STAGE IIB                              0                               8
  STAGE IIC                              1                               0
  STAGE III                              4                              17
  STAGE IIIA                             6                               7
  STAGE IIIB                            12                              41
  STAGE IIIC                            11                              27
  STAGE IV                              17                              25
  STAGE IVA                              5                              11
  STAGE IVB                              1                               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                              T0+T1  T2  T3  T4
  DEL PEAK 25(10Q23.31) MUTATED       2  16  71  12
  DEL PEAK 25(10Q23.31) WILD-TYPE     9  60 223  36
D48V4, multiclass
       clus
vv      DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  T0+T1                             2                               9
  T2                               16                              60
  T3                               71                             223
  T4                               12                              36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 25(10Q23.31) MUTATED    49  29  24
  DEL PEAK 25(10Q23.31) WILD-TYPE 203  72  52
D48V5, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  N0                            49                             203
  N1                            29                              72
  N2                            24                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 25(10Q23.31) MUTATED    71  20   2   1   8
  DEL PEAK 25(10Q23.31) WILD-TYPE 249  30   5   0  37
D48V6, multiclass
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  M0                             71                             249
  M1                             20                              30
  M1A                             2                               5
  M1B                             1                               0
  MX                              8                              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    50  52
  DEL PEAK 25(10Q23.31) WILD-TYPE 153 175
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     50   52
  DEL PEAK 25(10Q23.31) WILD-TYPE  153  175
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  FEMALE                            50                             153
  MALE                              52                             175
[1] 2 2
[1] FALSE
D48V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    94   7
  DEL PEAK 25(10Q23.31) WILD-TYPE 279  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     94    7
  DEL PEAK 25(10Q23.31) WILD-TYPE  279   48
                               clus
vv                              DEL PEAK 25(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                     94
  COLON MUCINOUS ADENOCARCINOMA                             7
                               clus
vv                              DEL PEAK 25(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      279
  COLON MUCINOUS ADENOCARCINOMA                              48
[1] 2 2
[1] FALSE
D48V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED     2 100
  DEL PEAK 25(10Q23.31) WILD-TYPE   1 327
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED      2  100
  DEL PEAK 25(10Q23.31) WILD-TYPE    1  327
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  NO                              2                               1
  YES                           100                             327
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(10Q23.31) MUTATED    71   1  10   5
  DEL PEAK 25(10Q23.31) WILD-TYPE 234   2  14  19
D48V10, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  R0                            71                             234
  R1                             1                               2
  R2                            10                              14
  RX                             5                              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"
D48V11, 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                          10    55
  DEL PEAK 25(10Q23.31) WILD-TYPE                        31   156
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   10
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 25(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     31
  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(49) Variable = DEL PEAK 26(10Q25.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10Q25.2) MUTATED    74  27
  DEL PEAK 26(10Q25.2) WILD-TYPE 255  57
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           101                            312 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                            27                             57 
$`DEL PEAK 26(10Q25.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
        5.06        37.02        17.79        42.28        35.11        45.60 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.61        23.87        61.84        52.44         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3548 
        1.02         6.97         9.07        37.05        29.00        33.99 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3680 
       13.02        19.99         6.05         2.01        50.04        11.01 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3818 
       37.05        36.00         5.03        85.05         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 
       36.95        33.07         0.99        17.03        24.03         2.01 
TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       50.99         7.96        34.03        42.02         0.99        33.04 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
       26.01        39.06         0.92        41.00         1.02         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 
        0.43        14.50        16.31         5.52         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       62.79        29.56         3.19         3.29         0.26         1.35 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        2.01         8.02         8.02        29.06        22.03         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       11.08        10.06        17.75         7.92        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       10.13         9.04        13.41        13.32       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 
        6.12        35.97        11.11        16.24        33.67        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 
       36.72        36.00        26.04        91.79        46.75 

$`DEL PEAK 26(10Q25.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 
       46.65        43.76        43.43        23.38        44.91        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
TCGA-A6-6649 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-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       20.28        16.24        24.92         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        21.01        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-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-3681 TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.98        19.00        26.99        19.04         0.99        35.05 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       14.93        17.03         0.99        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        17.03         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 
        1.58         0.10         0.76         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         5.19 
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-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        2.14         3.25         0.07         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       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-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        13.05        11.01        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 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-A1DA 
       38.20       130.65        92.75        49.91        12.59         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        16.31        29.59         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        43.07        61.87        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 
       45.11        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-A50V 
       35.80        26.17        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                          0.20                           0.07 
  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 
                        17.750                         20.235 
[1] "0.2 - 140.4 (17.8)" "0.1 - 139.2 (20.2)"
[1] "hr=" "1.6"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(10Q25.2) MUTATED        11        0        7        24         0
  DEL PEAK 26(10Q25.2) WILD-TYPE      61        1       21       103         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q25.2) MUTATED           1         6          4         12
  DEL PEAK 26(10Q25.2) WILD-TYPE         0        15          9         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(10Q25.2) MUTATED           12       18         5         0
  DEL PEAK 26(10Q25.2) WILD-TYPE         26       24        11         1
D49V3, multiclass
            clus
vv           DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  STAGE I                              11                             61
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            24                            103
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             6                             15
  STAGE IIIA                            4                              9
  STAGE IIIB                           12                             41
  STAGE IIIC                           12                             26
  STAGE IV                             18                             24
  STAGE IVA                             5                             11
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 26(10Q25.2) MUTATED       2  13  76  12
  DEL PEAK 26(10Q25.2) WILD-TYPE     9  63 218  36
D49V4, multiclass
       clus
vv      DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  T0+T1                            2                              9
  T2                              13                             63
  T3                              76                            218
  T4                              12                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 26(10Q25.2) MUTATED    47  30  26
  DEL PEAK 26(10Q25.2) WILD-TYPE 205  71  50
D49V5, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  N0                           47                            205
  N1                           30                             71
  N2                           26                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 26(10Q25.2) MUTATED    72  20   3   0   8
  DEL PEAK 26(10Q25.2) WILD-TYPE 248  30   4   1  37
D49V6, multiclass
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  M0                            72                            248
  M1                            20                             30
  M1A                            3                              4
  M1B                            0                              1
  MX                             8                             37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    48  55
  DEL PEAK 26(10Q25.2) WILD-TYPE 155 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     48   55
  DEL PEAK 26(10Q25.2) WILD-TYPE  155  172
        clus
vv       DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  FEMALE                           48                            155
  MALE                             55                            172
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    95   8
  DEL PEAK 26(10Q25.2) WILD-TYPE 278  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     95    8
  DEL PEAK 26(10Q25.2) WILD-TYPE  278   47
                               clus
vv                              DEL PEAK 26(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                    95
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 26(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     278
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED     2 101
  DEL PEAK 26(10Q25.2) WILD-TYPE   1 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED      2  101
  DEL PEAK 26(10Q25.2) WILD-TYPE    1  326
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  NO                             2                              1
  YES                          101                            326
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10Q25.2) MUTATED    69   1  11   5
  DEL PEAK 26(10Q25.2) WILD-TYPE 236   2  13  19
D49V10, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  R0                           69                            236
  R1                            1                              2
  R2                           11                             13
  RX                            5                             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 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                          10    53
  DEL PEAK 26(10Q25.2) WILD-TYPE                        31   158
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 26(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    31
  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(50) Variable = DEL PEAK 27(12P13.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.2) MUTATED    38  16
  DEL PEAK 27(12P13.2) WILD-TYPE 291  68
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            54                            359 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            16                             68 
$`DEL PEAK 27(12P13.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
       37.02        17.79        45.60        34.65        36.53        30.44 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 
       24.69        20.28        61.84         9.63        26.01        33.99 
TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3688 TCGA-AA-3858 
       13.02        78.08         2.01        50.04        19.00        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A01F TCGA-AA-A01T 
       17.03        24.03         2.01        50.99        32.02        33.04 
TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-6606 
        2.96         1.58         1.02         0.43        16.31        11.74 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        2.14         0.07        48.20         8.02         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 
       29.03        15.02        11.01        11.08        10.06         1.32 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 
       15.12         7.53        13.41        11.38        13.32        12.59 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
       13.38        11.11        16.24        61.87        36.72        36.00 

$`DEL PEAK 27(12P13.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        46.65        43.76        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       16.04        14.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       19.66        16.24        24.92        52.44         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-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-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        21.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         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-AZ-4308 
        0.20        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-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-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-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       13.02        14.04        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91       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-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18         8.61        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        74.56        43.07        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       55.04        51.75        45.11        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         15.68                          20.61 
[1] "0.1 - 78.1 (15.7)"  "0.1 - 140.4 (20.6)"
[1] "hr=" "1.9"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.2) MUTATED         9        0        2         8         1
  DEL PEAK 27(12P13.2) WILD-TYPE      63        1       26       119         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.2) MUTATED           0         2          1          7
  DEL PEAK 27(12P13.2) WILD-TYPE         1        19         12         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(12P13.2) MUTATED           10       10         2         0
  DEL PEAK 27(12P13.2) WILD-TYPE         28       32        14         1
D50V3, multiclass
            clus
vv           DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              2                             26
  STAGE IIA                             8                            119
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             2                             19
  STAGE IIIA                            1                             12
  STAGE IIIB                            7                             46
  STAGE IIIC                           10                             28
  STAGE IV                             10                             32
  STAGE IVA                             2                             14
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 27(12P13.2) MUTATED       2   8  39   5
  DEL PEAK 27(12P13.2) WILD-TYPE     9  68 255  43
D50V4, multiclass
       clus
vv      DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  T0+T1                            2                              9
  T2                               8                             68
  T3                              39                            255
  T4                               5                             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 27(12P13.2) MUTATED    23  18  13
  DEL PEAK 27(12P13.2) WILD-TYPE 229  83  63
D50V5, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  N0                           23                            229
  N1                           18                             83
  N2                           13                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 27(12P13.2) MUTATED    34  11   1   0   7
  DEL PEAK 27(12P13.2) WILD-TYPE 286  39   6   1  38
D50V6, multiclass
     clus
vv    DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  M0                            34                            286
  M1                            11                             39
  M1A                            1                              6
  M1B                            0                              1
  MX                             7                             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    27  27
  DEL PEAK 27(12P13.2) WILD-TYPE 176 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     27   27
  DEL PEAK 27(12P13.2) WILD-TYPE  176  200
        clus
vv       DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  FEMALE                           27                            176
  MALE                             27                            200
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    53   1
  DEL PEAK 27(12P13.2) WILD-TYPE 320  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     53    1
  DEL PEAK 27(12P13.2) WILD-TYPE  320   54
                               clus
vv                              DEL PEAK 27(12P13.2) MUTATED
  COLON ADENOCARCINOMA                                    53
  COLON MUCINOUS ADENOCARCINOMA                            1
                               clus
vv                              DEL PEAK 27(12P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     320
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED     0  54
  DEL PEAK 27(12P13.2) WILD-TYPE   3 373
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED      0   54
  DEL PEAK 27(12P13.2) WILD-TYPE    3  373
     clus
vv    DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  NO                             0                              3
  YES                           54                            373
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.2) MUTATED    37   1   4   4
  DEL PEAK 27(12P13.2) WILD-TYPE 268   2  20  20
D50V10, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  R0                           37                            268
  R1                            1                              2
  R2                            4                             20
  RX                            4                             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 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                           5    32
  DEL PEAK 27(12P13.2) WILD-TYPE                        36   179
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 27(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    36
  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(51) Variable = DEL PEAK 28(13Q14.13) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(13Q14.13) MUTATED    13   4
  DEL PEAK 28(13Q14.13) WILD-TYPE 316  80
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                             17                             396 
  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                              4                              80 
$`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 
       13.05        12.59        11.11         1.55        46.75 

$`DEL PEAK 28(13Q14.13) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       15.52        37.05        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        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        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        14.01        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 
       19.99        61.02        78.08         6.05         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-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        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        75.25        50.37         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        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-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.01         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        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         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE 
                           0.20                            0.07 
  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 
                          21.99                           19.99 
[1] "0.2 - 83.8 (22.0)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "1.1"
D51V2, 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      68        1       26       122         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(13Q14.13) MUTATED           0         0          0          0
  DEL PEAK 28(13Q14.13) WILD-TYPE         1        21         13         53
                                 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         34       41        16         0
D51V3, multiclass
            clus
vv           DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  STAGE I                                4                              68
  STAGE IA                               0                               1
  STAGE II                               2                              26
  STAGE IIA                              5                             122
  STAGE IIB                              0                               8
  STAGE IIC                              0                               1
  STAGE III                              0                              21
  STAGE IIIA                             0                              13
  STAGE IIIB                             0                              53
  STAGE IIIC                             4                              34
  STAGE IV                               1                              41
  STAGE IVA                              0                              16
  STAGE IVB                              1                               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                              T0+T1  T2  T3  T4
  DEL PEAK 28(13Q14.13) MUTATED       1   3  12   2
  DEL PEAK 28(13Q14.13) WILD-TYPE    10  73 282  46
D51V4, multiclass
       clus
vv      DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  T0+T1                             1                              10
  T2                                3                              73
  T3                               12                             282
  T4                                2                              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 28(13Q14.13) MUTATED    11   1   6
  DEL PEAK 28(13Q14.13) WILD-TYPE 241 100  70
D51V5, multiclass
    clus
vv   DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  N0                            11                             241
  N1                             1                             100
  N2                             6                              70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 28(13Q14.13) MUTATED    12   1   0   1   2
  DEL PEAK 28(13Q14.13) WILD-TYPE 308  49   7   0  43
D51V6, multiclass
     clus
vv    DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  M0                             12                             308
  M1                              1                              49
  M1A                             0                               7
  M1B                             1                               0
  MX                              2                              43
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED     8  10
  DEL PEAK 28(13Q14.13) WILD-TYPE 195 217
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED      8   10
  DEL PEAK 28(13Q14.13) WILD-TYPE  195  217
        clus
vv       DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  FEMALE                             8                             195
  MALE                              10                             217
[1] 2 2
[1] FALSE
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED    15   2
  DEL PEAK 28(13Q14.13) WILD-TYPE 358  53
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED     15    2
  DEL PEAK 28(13Q14.13) WILD-TYPE  358   53
                               clus
vv                              DEL PEAK 28(13Q14.13) MUTATED
  COLON ADENOCARCINOMA                                     15
  COLON MUCINOUS ADENOCARCINOMA                             2
                               clus
vv                              DEL PEAK 28(13Q14.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      358
  COLON MUCINOUS ADENOCARCINOMA                              53
[1] 2 2
[1] FALSE
D51V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q14.13) MUTATED     0  18
  DEL PEAK 28(13Q14.13) WILD-TYPE   3 409
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q14.13) MUTATED      0   18
  DEL PEAK 28(13Q14.13) WILD-TYPE    3  409
     clus
vv    DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  NO                              0                               3
  YES                            18                             409
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(13Q14.13) MUTATED    15   0   0   1
  DEL PEAK 28(13Q14.13) WILD-TYPE 290   3  24  23
D51V10, multiclass
    clus
vv   DEL PEAK 28(13Q14.13) MUTATED DEL PEAK 28(13Q14.13) WILD-TYPE
  R0                            15                             290
  R1                             0                               3
  R2                             0                              24
  RX                             1                              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"
D51V11, 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                           2     8
  DEL PEAK 28(13Q14.13) WILD-TYPE                        39   203
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 28(13Q14.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                        8
                                  clus
vv                                 DEL PEAK 28(13Q14.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     39
  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(52) Variable = DEL PEAK 29(14Q31.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(14Q31.1) MUTATED   109  28
  DEL PEAK 29(14Q31.1) WILD-TYPE 220  56
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                           137                            276 
  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                            28                             56 
$`DEL PEAK 29(14Q31.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 
       37.02        42.28        35.11        45.60        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       36.53        14.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13        25.08        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 
       24.69        23.87        20.28        61.84         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        24.03        19.07        19.07        34.03 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       12.99        13.02        23.01        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01        15.02        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05         0.99        25.02        36.95        37.02        17.03 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       31.07        17.03        24.03        18.05         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       24.00         7.96        17.03        27.02        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       21.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         1.58         1.02         0.10 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
        0.43        14.50         0.95        15.75         0.20         5.52 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
       75.25         1.41         5.65        22.36        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 
        1.94         3.06         2.14         0.07         0.26        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5868 TCGA-CM-6163 
        2.01         8.02         8.02        27.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       29.03        13.02        15.02        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       14.99        12.26        13.51        18.25         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 
       14.30        13.41        11.38        38.20        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 
        7.50       131.51        14.04       119.93        35.97        13.38 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 
       29.59        33.67         1.28         0.53         8.35        82.39 
TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       36.72        91.79         4.11         5.06         5.59 

$`DEL PEAK 29(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       44.91        13.94        37.05        37.25        16.04        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        25.18        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        52.44         9.63         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        37.05        36.03         8.05 
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-3558 TCGA-AA-3560 
       21.01        24.00        17.95        29.95        20.98        19.99 
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-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.05        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       15.95        38.99        14.93         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       34.03         2.01        13.05        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       18.05        18.05         4.01         0.99        17.03        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
       16.31        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.25         3.29         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        26.04        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        11.01        12.03 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       19.59        11.51        20.19        20.42        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
      130.65        92.75        49.91        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G 
        7.76       139.17         6.12        26.47        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.00        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-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       52.80         2.79         5.98        26.99        17.29        14.76 

  DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE 
                          0.07                           0.07 
  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 
                        17.030                         20.995 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (21.0)"
[1] "hr=" "1.2"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(14Q31.1) MUTATED        21        0        7        34         1
  DEL PEAK 29(14Q31.1) WILD-TYPE      51        1       21        93         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q31.1) MUTATED           0         9          5         18
  DEL PEAK 29(14Q31.1) WILD-TYPE         1        12          8         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(14Q31.1) MUTATED           14       19         9         1
  DEL PEAK 29(14Q31.1) WILD-TYPE         24       23         7         0
D52V3, multiclass
            clus
vv           DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  STAGE I                              21                             51
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            34                             93
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             9                             12
  STAGE IIIA                            5                              8
  STAGE IIIB                           18                             35
  STAGE IIIC                           14                             24
  STAGE IV                             19                             23
  STAGE IVA                             9                              7
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 29(14Q31.1) MUTATED       6  22 100  13
  DEL PEAK 29(14Q31.1) WILD-TYPE     5  54 194  35
D52V4, multiclass
       clus
vv      DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  T0+T1                            6                              5
  T2                              22                             54
  T3                             100                            194
  T4                              13                             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 29(14Q31.1) MUTATED    71  41  29
  DEL PEAK 29(14Q31.1) WILD-TYPE 181  60  47
D52V5, multiclass
    clus
vv   DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  N0                           71                            181
  N1                           41                             60
  N2                           29                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 29(14Q31.1) MUTATED    98  25   3   1  12
  DEL PEAK 29(14Q31.1) WILD-TYPE 222  25   4   0  33
D52V6, multiclass
     clus
vv    DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  M0                            98                            222
  M1                            25                             25
  M1A                            3                              4
  M1B                            1                              0
  MX                            12                             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED    64  77
  DEL PEAK 29(14Q31.1) WILD-TYPE 139 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED     64   77
  DEL PEAK 29(14Q31.1) WILD-TYPE  139  150
        clus
vv       DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  FEMALE                           64                            139
  MALE                             77                            150
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED   134   5
  DEL PEAK 29(14Q31.1) WILD-TYPE 239  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED    134    5
  DEL PEAK 29(14Q31.1) WILD-TYPE  239   50
                               clus
vv                              DEL PEAK 29(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   134
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 29(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     239
  COLON MUCINOUS ADENOCARCINOMA                             50
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q31.1) MUTATED     0 141
  DEL PEAK 29(14Q31.1) WILD-TYPE   3 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q31.1) MUTATED      0  141
  DEL PEAK 29(14Q31.1) WILD-TYPE    3  286
     clus
vv    DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  NO                             0                              3
  YES                          141                            286
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(14Q31.1) MUTATED    93   0  11   8
  DEL PEAK 29(14Q31.1) WILD-TYPE 212   3  13  16
D52V10, multiclass
    clus
vv   DEL PEAK 29(14Q31.1) MUTATED DEL PEAK 29(14Q31.1) WILD-TYPE
  R0                           93                            212
  R1                            0                              3
  R2                           11                             13
  RX                            8                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, 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                          12    68
  DEL PEAK 29(14Q31.1) WILD-TYPE                        29   143
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      68
                                  clus
vv                                 DEL PEAK 29(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    29
  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(53) Variable = DEL PEAK 30(15Q11.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(15Q11.2) MUTATED   127  33
  DEL PEAK 30(15Q11.2) WILD-TYPE 202  51
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                           160                            253 
  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                            33                             51 
$`DEL PEAK 30(15Q11.2) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 
       43.76        43.43        17.79        42.28        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       15.52        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       29.19        29.16        22.52        25.08        20.61        21.76 
TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.12        20.28        61.84        52.44         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
        1.02         6.97        37.05        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 
       19.99         2.01        50.04        47.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05         1.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       24.03        27.02        29.98        12.99         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        32.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       41.00         1.58         1.02         0.10         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4681 
       14.50        16.31         0.95        15.75         5.52        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        61.41        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 
        2.14         0.26         1.35       102.44        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
        8.02        27.02        13.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 
       17.03        14.04        29.03        16.04        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       20.19        17.75         1.32        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
        7.53        10.13         9.04        11.38       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 
       13.32        12.59       140.38         7.50       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
       14.04        35.97        95.18        13.38        35.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 
       16.24        33.67         1.28         0.53        35.41        28.21 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
        8.35        43.07        61.87        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V 
       36.00        91.79        46.75         5.06 

$`DEL PEAK 30(15Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 
        5.06        37.02        46.65        23.38        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        16.04        14.53        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 
       19.66        16.24        24.92         9.63         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
        0.99         0.99        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       15.95        14.93        33.07        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 
       24.00         2.01        20.98        34.03        16.08        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       21.99        34.98         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
       56.55         0.79         0.72         0.76         0.20         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
       27.09         0.20        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-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        21.01         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        14.99        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         7.92        17.85         4.50        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-QG-A5YV TCGA-QG-A5YX 
        4.11         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE 
                          0.10                           0.07 
  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 
                        20.155                         19.590 
[1] "0.1 - 140.4 (20.2)" "0.1 - 139.2 (19.6)"
[1] "hr=" "1"  
D53V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(15Q11.2) MUTATED        27        0        7        40         2
  DEL PEAK 30(15Q11.2) WILD-TYPE      45        1       21        87         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(15Q11.2) MUTATED           0         6          8         21
  DEL PEAK 30(15Q11.2) WILD-TYPE         1        15          5         32
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(15Q11.2) MUTATED           19       22         9         1
  DEL PEAK 30(15Q11.2) WILD-TYPE         19       20         7         0
D53V3, multiclass
            clus
vv           DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  STAGE I                              27                             45
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             87
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            8                              5
  STAGE IIIB                           21                             32
  STAGE IIIC                           19                             19
  STAGE IV                             22                             20
  STAGE IVA                             9                              7
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 30(15Q11.2) MUTATED       5  29 114  18
  DEL PEAK 30(15Q11.2) WILD-TYPE     6  47 180  30
D53V4, multiclass
       clus
vv      DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  T0+T1                            5                              6
  T2                              29                             47
  T3                             114                            180
  T4                              18                             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 30(15Q11.2) MUTATED    83  47  36
  DEL PEAK 30(15Q11.2) WILD-TYPE 169  54  40
D53V5, multiclass
    clus
vv   DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  N0                           83                            169
  N1                           47                             54
  N2                           36                             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 30(15Q11.2) MUTATED   115  26   5   1  16
  DEL PEAK 30(15Q11.2) WILD-TYPE 205  24   2   0  29
D53V6, multiclass
     clus
vv    DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  M0                           115                            205
  M1                            26                             24
  M1A                            5                              2
  M1B                            1                              0
  MX                            16                             29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED    77  89
  DEL PEAK 30(15Q11.2) WILD-TYPE 126 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED     77   89
  DEL PEAK 30(15Q11.2) WILD-TYPE  126  138
        clus
vv       DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  FEMALE                           77                            126
  MALE                             89                            138
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED   151  13
  DEL PEAK 30(15Q11.2) WILD-TYPE 222  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED    151   13
  DEL PEAK 30(15Q11.2) WILD-TYPE  222   42
                               clus
vv                              DEL PEAK 30(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   151
  COLON MUCINOUS ADENOCARCINOMA                           13
                               clus
vv                              DEL PEAK 30(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     222
  COLON MUCINOUS ADENOCARCINOMA                             42
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q11.2) MUTATED     3 163
  DEL PEAK 30(15Q11.2) WILD-TYPE   0 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q11.2) MUTATED      3  163
  DEL PEAK 30(15Q11.2) WILD-TYPE    0  264
     clus
vv    DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  NO                             3                              0
  YES                          163                            264
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(15Q11.2) MUTATED   114   1  12   7
  DEL PEAK 30(15Q11.2) WILD-TYPE 191   2  12  17
D53V10, multiclass
    clus
vv   DEL PEAK 30(15Q11.2) MUTATED DEL PEAK 30(15Q11.2) WILD-TYPE
  R0                          114                            191
  R1                            1                              2
  R2                           12                             12
  RX                            7                             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"
D53V11, 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                          11    89
  DEL PEAK 30(15Q11.2) WILD-TYPE                        30   122
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 30(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK 30(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    30
  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(54) Variable = DEL PEAK 31(15Q15.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q15.2) MUTATED   124  31
  DEL PEAK 31(15Q15.2) WILD-TYPE 205  53
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                           155                            258 
  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                            31                             53 
$`DEL PEAK 31(15Q15.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       44.91        45.60        15.52        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.91        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        20.12        20.28        61.84        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 
        5.03         1.02         1.02         6.97         9.07        37.05 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
       23.01        19.99        19.99         2.01        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
       11.01        37.05        19.00        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
        0.99        31.07        17.03        24.03        29.98        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 
        2.01        21.99        50.99        13.05        34.06        24.00 
TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4681 
       16.31         0.95        15.75         0.20         5.52        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        61.41        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 
        2.14         0.26       102.44        48.20         2.01         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       27.02        13.02        29.06         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        16.04        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 
       11.08        11.01        10.06        12.03        12.26        20.19 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
        1.32        15.12         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.38       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      131.51         6.12        35.97        95.18        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       28.21         8.35        61.87        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V 
       36.00        26.04        91.79        46.75         5.06 

$`DEL PEAK 31(15Q15.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       46.65        23.38        35.11        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       16.04        14.53        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       24.16        24.69        24.39        23.87        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.92         9.63         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       29.00        29.00        26.01         0.99        17.95        29.95 
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-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01         0.92        47.05        15.02         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        26.99        19.04         0.99         0.99        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-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 
       20.98        34.03        16.08        26.01        25.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        17.03         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98         0.99        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.92        27.09        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-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-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-6751 
       15.62        51.32        21.99        21.01         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 
       23.05        20.02        37.02        26.04         8.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.95        14.99        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25         7.92        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14        15.58        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        24.43        38.20        49.91         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 
      119.93        60.79       117.07        98.24         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 
       13.64        13.45         6.18        16.31        29.59        19.43 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      107.67        82.39        23.51        74.56        43.07        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-G4-6323 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         4.11 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 

  DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE 
                          0.10                           0.07 
  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 
                         20.19                          19.51 
[1] "0.1 - 140.4 (20.2)" "0.1 - 139.2 (19.5)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q15.2) MUTATED        27        0        7        37         2
  DEL PEAK 31(15Q15.2) WILD-TYPE      45        1       21        90         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q15.2) MUTATED           0         6          6         20
  DEL PEAK 31(15Q15.2) WILD-TYPE         1        15          7         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q15.2) MUTATED           18       24         8         1
  DEL PEAK 31(15Q15.2) WILD-TYPE         20       18         8         0
D54V3, multiclass
            clus
vv           DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  STAGE I                              27                             45
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            37                             90
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              7
  STAGE IIIB                           20                             33
  STAGE IIIC                           18                             20
  STAGE IV                             24                             18
  STAGE IVA                             8                              8
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 31(15Q15.2) MUTATED       5  28 110  17
  DEL PEAK 31(15Q15.2) WILD-TYPE     6  48 184  31
D54V4, multiclass
       clus
vv      DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  T0+T1                            5                              6
  T2                              28                             48
  T3                             110                            184
  T4                              17                             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 31(15Q15.2) MUTATED    79  48  33
  DEL PEAK 31(15Q15.2) WILD-TYPE 173  53  43
D54V5, multiclass
    clus
vv   DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  N0                           79                            173
  N1                           48                             53
  N2                           33                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 31(15Q15.2) MUTATED   106  27   5   1  17
  DEL PEAK 31(15Q15.2) WILD-TYPE 214  23   2   0  28
D54V6, multiclass
     clus
vv    DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  M0                           106                            214
  M1                            27                             23
  M1A                            5                              2
  M1B                            1                              0
  MX                            17                             28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED    74  86
  DEL PEAK 31(15Q15.2) WILD-TYPE 129 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED     74   86
  DEL PEAK 31(15Q15.2) WILD-TYPE  129  141
        clus
vv       DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  FEMALE                           74                            129
  MALE                             86                            141
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED   146  12
  DEL PEAK 31(15Q15.2) WILD-TYPE 227  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED    146   12
  DEL PEAK 31(15Q15.2) WILD-TYPE  227   43
                               clus
vv                              DEL PEAK 31(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                   146
  COLON MUCINOUS ADENOCARCINOMA                           12
                               clus
vv                              DEL PEAK 31(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     227
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q15.2) MUTATED     3 157
  DEL PEAK 31(15Q15.2) WILD-TYPE   0 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q15.2) MUTATED      3  157
  DEL PEAK 31(15Q15.2) WILD-TYPE    0  270
     clus
vv    DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  NO                             3                              0
  YES                          157                            270
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q15.2) MUTATED   111   1  12   6
  DEL PEAK 31(15Q15.2) WILD-TYPE 194   2  12  18
D54V10, multiclass
    clus
vv   DEL PEAK 31(15Q15.2) MUTATED DEL PEAK 31(15Q15.2) WILD-TYPE
  R0                          111                            194
  R1                            1                              2
  R2                           12                             12
  RX                            6                             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"
D54V11, 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                          12    86
  DEL PEAK 31(15Q15.2) WILD-TYPE                        29   125
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 31(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    29
  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(55) Variable = DEL PEAK 32(15Q21.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q21.1) MUTATED   124  28
  DEL PEAK 32(15Q21.1) WILD-TYPE 205  56
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                           152                            261 
  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                            28                             56 
$`DEL PEAK 32(15Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       37.02        43.76        43.43        23.38        17.79        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       45.60        15.52        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 
       30.44        29.19        29.16        22.52        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       21.76        20.12        20.28        61.84         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        1.02         6.97         9.07        37.05        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       19.99        19.99         2.01        50.04        47.01        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 
       37.05        19.00        36.00        85.05        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 
       31.07        17.03        24.03        29.98        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 
       21.99        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        30.02        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       15.75         0.20         5.52        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       61.41        29.56         5.23         3.19         2.14         0.26 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
      102.44        48.20         2.01         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       16.04        15.02        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       10.06        12.03        12.26        20.19         1.32        15.12 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       92.75        13.32        12.59       140.38       131.51         6.12 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       35.97        95.18        13.38        35.87         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67         1.28         0.53        35.41         8.35        61.87 
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-A50V 
       46.75         5.06 

$`DEL PEAK 32(15Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
        5.06        46.65        42.28        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       37.25        16.04        14.53        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        23.87        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 
       16.24        24.92        52.44         9.63         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-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-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
        6.97        54.02        14.01         0.92        47.05        15.02 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.98         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        32.05        31.07        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 
        2.01        20.98        34.03        16.08        26.01        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00J 
       19.07         7.96        27.02        13.94        38.04        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        17.03         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98         0.99        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       32.94         5.13        22.36        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.93       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 
       13.02        14.04        11.01        12.95        14.99        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       13.51        11.51        20.42        17.75        18.25         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        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        43.07        53.62        44.68        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       35.93        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         4.11         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE 
                          0.10                           0.07 
  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 
                        20.445                         19.070 
[1] "0.1 - 140.4 (20.4)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.2"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q21.1) MUTATED        25        0        7        40         3
  DEL PEAK 32(15Q21.1) WILD-TYPE      47        1       21        87         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q21.1) MUTATED           0         6          6         18
  DEL PEAK 32(15Q21.1) WILD-TYPE         1        15          7         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q21.1) MUTATED           17       23         8         1
  DEL PEAK 32(15Q21.1) WILD-TYPE         21       19         8         0
D55V3, multiclass
            clus
vv           DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  STAGE I                              25                             47
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             87
  STAGE IIB                             3                              5
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              7
  STAGE IIIB                           18                             35
  STAGE IIIC                           17                             21
  STAGE IV                             23                             19
  STAGE IVA                             8                              8
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 32(15Q21.1) MUTATED       4  27 109  18
  DEL PEAK 32(15Q21.1) WILD-TYPE     7  49 185  30
D55V4, multiclass
       clus
vv      DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  T0+T1                            4                              7
  T2                              27                             49
  T3                             109                            185
  T4                              18                             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 32(15Q21.1) MUTATED    81  45  32
  DEL PEAK 32(15Q21.1) WILD-TYPE 171  56  44
D55V5, multiclass
    clus
vv   DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  N0                           81                            171
  N1                           45                             56
  N2                           32                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 32(15Q21.1) MUTATED   106  26   5   1  17
  DEL PEAK 32(15Q21.1) WILD-TYPE 214  24   2   0  28
D55V6, multiclass
     clus
vv    DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  M0                           106                            214
  M1                            26                             24
  M1A                            5                              2
  M1B                            1                              0
  MX                            17                             28
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED    72  86
  DEL PEAK 32(15Q21.1) WILD-TYPE 131 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED     72   86
  DEL PEAK 32(15Q21.1) WILD-TYPE  131  141
        clus
vv       DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  FEMALE                           72                            131
  MALE                             86                            141
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED   145  12
  DEL PEAK 32(15Q21.1) WILD-TYPE 228  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED    145   12
  DEL PEAK 32(15Q21.1) WILD-TYPE  228   43
                               clus
vv                              DEL PEAK 32(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                   145
  COLON MUCINOUS ADENOCARCINOMA                           12
                               clus
vv                              DEL PEAK 32(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     228
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q21.1) MUTATED     3 155
  DEL PEAK 32(15Q21.1) WILD-TYPE   0 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q21.1) MUTATED      3  155
  DEL PEAK 32(15Q21.1) WILD-TYPE    0  272
     clus
vv    DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  NO                             3                              0
  YES                          155                            272
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q21.1) MUTATED   110   0  12   6
  DEL PEAK 32(15Q21.1) WILD-TYPE 195   3  12  18
D55V10, multiclass
    clus
vv   DEL PEAK 32(15Q21.1) MUTATED DEL PEAK 32(15Q21.1) WILD-TYPE
  R0                          110                            195
  R1                            0                              3
  R2                           12                             12
  RX                            6                             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 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                           9    84
  DEL PEAK 32(15Q21.1) WILD-TYPE                        32   127
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      84
                                  clus
vv                                 DEL PEAK 32(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    32
  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(56) Variable = DEL PEAK 33(15Q22.33) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(15Q22.33) MUTATED   120  28
  DEL PEAK 33(15Q22.33) WILD-TYPE 209  56
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                            148                             265 
  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                             28                              56 
$`DEL PEAK 33(15Q22.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 
       37.02        43.76        43.43        17.79        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       15.52        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       23.61        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         1.02         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         0.99         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-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02W 
       31.00        33.04        26.01        37.02         2.96        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        1.58         1.02         0.10         0.43         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4681 
       16.31         0.95        15.75         0.20         5.52        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        61.41        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        2.14         0.26       102.44        48.20        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
        8.02        27.02        13.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 
       17.03        14.04        29.03        16.04        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 
       11.08        11.01        10.06        12.03        20.19         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       15.12        17.13        12.49         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       13.41        11.38       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6460 
       12.59       140.38       131.51         6.12        95.18        13.38 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       35.41         8.35        61.87        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V 
       36.00        91.79        46.75         5.06 

$`DEL PEAK 33(15Q22.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 
        5.06        46.65        23.38        42.28        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        16.04        14.53        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       33.53        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 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-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        52.44         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
        0.99        14.01        24.00        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.98         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       14.93        33.07        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        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       27.02         0.99        34.98         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.92        27.09        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-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-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-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.01         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-CM-6675 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       12.95        13.05        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.50        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       24.43        38.20         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 
       13.45         6.18        16.31        29.59        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       28.21        82.39        23.51        74.56        43.07        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-QG-A5YV TCGA-QG-A5YX 
        4.11         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE 
                           0.10                            0.07 
  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 
                          20.09                           19.66 
[1] "0.1 - 140.4 (20.1)" "0.1 - 139.2 (19.7)"
[1] "hr=" "1.2"
D56V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q22.33) MUTATED        22        0        7        38         2
  DEL PEAK 33(15Q22.33) WILD-TYPE      50        1       21        89         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q22.33) MUTATED           0         5          7         17
  DEL PEAK 33(15Q22.33) WILD-TYPE         1        16          6         36
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q22.33) MUTATED           18       22        10         0
  DEL PEAK 33(15Q22.33) WILD-TYPE         20       20         6         1
D56V3, multiclass
            clus
vv           DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  STAGE I                               22                              50
  STAGE IA                               0                               1
  STAGE II                               7                              21
  STAGE IIA                             38                              89
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             7                               6
  STAGE IIIB                            17                              36
  STAGE IIIC                            18                              20
  STAGE IV                              22                              20
  STAGE IVA                             10                               6
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 33(15Q22.33) MUTATED       5  22 109  16
  DEL PEAK 33(15Q22.33) WILD-TYPE     6  54 185  32
D56V4, multiclass
       clus
vv      DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  T0+T1                             5                               6
  T2                               22                              54
  T3                              109                             185
  T4                               16                              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 33(15Q22.33) MUTATED    76  42  34
  DEL PEAK 33(15Q22.33) WILD-TYPE 176  59  42
D56V5, multiclass
    clus
vv   DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  N0                            76                             176
  N1                            42                              59
  N2                            34                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 33(15Q22.33) MUTATED   100  27   5   0  16
  DEL PEAK 33(15Q22.33) WILD-TYPE 220  23   2   1  29
D56V6, multiclass
     clus
vv    DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  M0                            100                             220
  M1                             27                              23
  M1A                             5                               2
  M1B                             0                               1
  MX                             16                              29
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED    69  83
  DEL PEAK 33(15Q22.33) WILD-TYPE 134 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED     69   83
  DEL PEAK 33(15Q22.33) WILD-TYPE  134  144
        clus
vv       DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  FEMALE                            69                             134
  MALE                              83                             144
[1] 2 2
[1] FALSE
D56V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED   140  10
  DEL PEAK 33(15Q22.33) WILD-TYPE 233  45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED    140   10
  DEL PEAK 33(15Q22.33) WILD-TYPE  233   45
                               clus
vv                              DEL PEAK 33(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                    140
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              DEL PEAK 33(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      233
  COLON MUCINOUS ADENOCARCINOMA                              45
[1] 2 2
[1] FALSE
D56V9, binary
                                 cls
clus                                0   1
  DEL PEAK 33(15Q22.33) MUTATED     3 149
  DEL PEAK 33(15Q22.33) WILD-TYPE   0 278
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(15Q22.33) MUTATED      3  149
  DEL PEAK 33(15Q22.33) WILD-TYPE    0  278
     clus
vv    DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  NO                              3                               0
  YES                           149                             278
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(15Q22.33) MUTATED   104   1  11   7
  DEL PEAK 33(15Q22.33) WILD-TYPE 201   2  13  17
D56V10, multiclass
    clus
vv   DEL PEAK 33(15Q22.33) MUTATED DEL PEAK 33(15Q22.33) WILD-TYPE
  R0                           104                             201
  R1                             1                               2
  R2                            11                              13
  RX                             7                              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"
D56V11, 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                           9    85
  DEL PEAK 33(15Q22.33) WILD-TYPE                        32   126
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       85
                                  clus
vv                                 DEL PEAK 33(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     32
  WHITE                                                        126
[1] 4 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 34(16P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16P13.3) MUTATED    33  17
  DEL PEAK 34(16P13.3) WILD-TYPE 296  67
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            50                            363 
  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                            17                             67 
$`DEL PEAK 34(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 
       17.79        44.91        45.60        34.65        14.53        21.76 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 
       61.84         5.03        13.02        54.02        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 
       36.95        31.07         2.01        33.01         2.01         2.01 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F TCGA-AA-A02Y TCGA-AD-A5EK 
       27.02        34.03        27.02        39.98        39.98         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
        0.46        14.50        16.31         0.20         5.52         5.65 
TCGA-AZ-6607 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
        3.19        13.02        22.03        22.98         5.03        15.02 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       16.04        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 TCGA-G4-6294 TCGA-G4-6626 
       49.91        12.59        44.32         8.61        28.21        46.75 
TCGA-NH-A50T TCGA-QG-A5YV 
        4.11        26.99 

$`DEL PEAK 34(16P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        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-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        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        17.03         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-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         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        1.02         0.10         0.76         0.20         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.95        15.75        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        2.24         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         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-5341 
       37.02         8.02        26.04         8.02        27.02        29.06 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        20.42        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-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-F4-6460 
       35.97        60.79       117.07        98.24        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       91.79        47.15        52.80         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.59        17.29        14.76 

  DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE 
                          0.20                           0.07 
  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 
                         17.77                          20.02 
[1] "0.2 - 61.8 (17.8)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "2.2"
D57V2, 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      69        1       25       111         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(16P13.3) MUTATED           0         0          0          8
  DEL PEAK 34(16P13.3) WILD-TYPE         1        21         13         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(16P13.3) MUTATED            9        6         4         0
  DEL PEAK 34(16P13.3) WILD-TYPE         29       36        12         1
D57V3, multiclass
            clus
vv           DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  STAGE I                               3                             69
  STAGE IA                              0                              1
  STAGE II                              3                             25
  STAGE IIA                            16                            111
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             0                             21
  STAGE IIIA                            0                             13
  STAGE IIIB                            8                             45
  STAGE IIIC                            9                             29
  STAGE IV                              6                             36
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 34(16P13.3) MUTATED       0   3  43   6
  DEL PEAK 34(16P13.3) WILD-TYPE    11  73 251  42
D57V4, multiclass
       clus
vv      DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  T0+T1                            0                             11
  T2                               3                             73
  T3                              43                            251
  T4                               6                             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 34(16P13.3) MUTATED    24  15  13
  DEL PEAK 34(16P13.3) WILD-TYPE 228  86  63
D57V5, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  N0                           24                            228
  N1                           15                             86
  N2                           13                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 34(16P13.3) MUTATED    34   8   2   0   5
  DEL PEAK 34(16P13.3) WILD-TYPE 286  42   5   1  40
D57V6, multiclass
     clus
vv    DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  M0                            34                            286
  M1                             8                             42
  M1A                            2                              5
  M1B                            0                              1
  MX                             5                             40
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    24  28
  DEL PEAK 34(16P13.3) WILD-TYPE 179 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     24   28
  DEL PEAK 34(16P13.3) WILD-TYPE  179  199
        clus
vv       DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  FEMALE                           24                            179
  MALE                             28                            199
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED    46   6
  DEL PEAK 34(16P13.3) WILD-TYPE 327  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED     46    6
  DEL PEAK 34(16P13.3) WILD-TYPE  327   49
                               clus
vv                              DEL PEAK 34(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                    46
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              DEL PEAK 34(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     327
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(16P13.3) MUTATED     0  52
  DEL PEAK 34(16P13.3) WILD-TYPE   3 375
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16P13.3) MUTATED      0   52
  DEL PEAK 34(16P13.3) WILD-TYPE    3  375
     clus
vv    DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  NO                             0                              3
  YES                           52                            375
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16P13.3) MUTATED    38   1   3   1
  DEL PEAK 34(16P13.3) WILD-TYPE 267   2  21  23
D57V10, multiclass
    clus
vv   DEL PEAK 34(16P13.3) MUTATED DEL PEAK 34(16P13.3) WILD-TYPE
  R0                           38                            267
  R1                            1                              2
  R2                            3                             21
  RX                            1                             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"
D57V11, 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                           8    27
  DEL PEAK 34(16P13.3) WILD-TYPE                        33   184
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 34(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK 34(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    33
  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(58) Variable = DEL PEAK 35(16Q23.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16Q23.1) MUTATED    40  15
  DEL PEAK 35(16Q23.1) WILD-TYPE 289  69
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            55                            358 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            15                             69 
$`DEL PEAK 35(16Q23.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-5660 TCGA-A6-5661 
       37.02        23.38        42.28        45.60        29.19        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-A565 TCGA-AA-3494 
       22.06        22.52        21.76        24.39        16.24         1.02 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3672 
        6.97        13.02         1.02         0.99        21.01         0.92 
TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       37.05        17.98        38.99        36.03        31.07        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A01P 
       33.01         2.01        21.99        30.02        18.05        38.07 
TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-A5EK TCGA-AY-A69D 
        1.02         2.96        22.03        41.00         0.43         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5254 
        5.65         5.13        49.41        12.10         3.19         2.24 
TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6678 
        3.29        22.03         5.03        15.02        13.02        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-NH-A50T 
       20.19        17.75        15.12        24.43         7.50         4.11 
TCGA-QG-A5Z2 
       14.76 

$`DEL PEAK 35(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        46.65        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        23.61        22.09        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 
       24.69        23.87        20.12        19.66        20.28        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-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-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         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-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       12.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        15.95        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
        0.99        33.07        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        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        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 
        1.58         1.02         0.10         0.76         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-AZ-4308 TCGA-AZ-4313 
        0.20        21.44        17.82         5.19        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-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.94         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       29.06        22.98        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-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        47.15        52.80         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59        26.99        17.29 

  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                          0.43                           0.07 
  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 
                         17.98                          20.07 
[1] "0.4 - 53.0 (18.0)"  "0.1 - 140.4 (20.1)"
[1] "hr=" "2"  
D58V2, 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      62        1       23       110         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(16Q23.1) MUTATED           0         3          0          7
  DEL PEAK 35(16Q23.1) WILD-TYPE         1        18         13         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(16Q23.1) MUTATED            3        6         3         0
  DEL PEAK 35(16Q23.1) WILD-TYPE         35       36        13         1
D58V3, multiclass
            clus
vv           DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  STAGE I                              10                             62
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            17                            110
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            0                             13
  STAGE IIIB                            7                             46
  STAGE IIIC                            3                             35
  STAGE IV                              6                             36
  STAGE IVA                             3                             13
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 35(16Q23.1) MUTATED       0  10  38   8
  DEL PEAK 35(16Q23.1) WILD-TYPE    11  66 256  40
D58V4, multiclass
       clus
vv      DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  T0+T1                            0                             11
  T2                              10                             66
  T3                              38                            256
  T4                               8                             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 35(16Q23.1) MUTATED    35  14   7
  DEL PEAK 35(16Q23.1) WILD-TYPE 217  87  69
D58V5, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  N0                           35                            217
  N1                           14                             87
  N2                            7                             69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 35(16Q23.1) MUTATED    40   7   2   0   7
  DEL PEAK 35(16Q23.1) WILD-TYPE 280  43   5   1  38
D58V6, multiclass
     clus
vv    DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  M0                            40                            280
  M1                             7                             43
  M1A                            2                              5
  M1B                            0                              1
  MX                             7                             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    31  25
  DEL PEAK 35(16Q23.1) WILD-TYPE 172 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     31   25
  DEL PEAK 35(16Q23.1) WILD-TYPE  172  202
        clus
vv       DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  FEMALE                           31                            172
  MALE                             25                            202
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    47   9
  DEL PEAK 35(16Q23.1) WILD-TYPE 326  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     47    9
  DEL PEAK 35(16Q23.1) WILD-TYPE  326   46
                               clus
vv                              DEL PEAK 35(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                    47
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              DEL PEAK 35(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     326
  COLON MUCINOUS ADENOCARCINOMA                             46
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED     0  56
  DEL PEAK 35(16Q23.1) WILD-TYPE   3 371
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED      0   56
  DEL PEAK 35(16Q23.1) WILD-TYPE    3  371
     clus
vv    DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  NO                             0                              3
  YES                           56                            371
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16Q23.1) MUTATED    38   0   2   4
  DEL PEAK 35(16Q23.1) WILD-TYPE 267   3  22  20
D58V10, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  R0                           38                            267
  R1                            0                              3
  R2                            2                             22
  RX                            4                             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"
D58V11, 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                           9    22
  DEL PEAK 35(16Q23.1) WILD-TYPE                        32   189
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 35(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 35(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    32
  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(59) Variable = DEL PEAK 36(17P12) MUTATION ANALYSIS
D59V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 36(17P12) MUTATED   183  49
  DEL PEAK 36(17P12) WILD-TYPE 146  35
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                         232                          181 
  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                          49                           35 
$`DEL PEAK 36(17P12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        45.60        15.52        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       24.16        20.61        24.69        23.87        20.28        61.84 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.05         2.01        14.01        50.04        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 
        5.98        37.05        19.00        36.00        85.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       25.02        38.99        36.95        37.02         0.99        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05         2.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       24.00        27.02         7.96        19.00        34.03        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       37.02         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 
        0.95        15.75         0.20         5.52        75.25         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65         5.13        83.80        22.36        65.00        61.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       13.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       17.03        29.03        21.99        14.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        13.05        11.08        10.06        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        7.92        15.12        17.13        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      140.38        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 
       26.47       119.93        35.97       117.07        13.38        11.11 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6298 
       16.31        16.24        33.67         1.28         8.35        23.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       61.87        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V 
       36.72        36.00        26.43        91.79        46.75         5.06 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59        26.99        17.29 

$`DEL PEAK 36(17P12) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 
       46.65        23.38        44.91        13.94        16.04        36.53 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       33.53        23.61        22.09        22.06         8.38        25.08 
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-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       52.44         9.63         3.02        35.01        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       13.02         1.02         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       29.00        26.01         0.99        17.95        29.95        20.98 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        15.02        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 
        1.02        17.98        15.95        14.93        17.03        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       24.00         2.01        13.05        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        34.98        15.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O 
       35.01        35.01        26.01        39.06        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.03        39.98        18.05         0.07        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.76         0.92        27.09        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       50.37        58.39        32.94        62.79        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
      100.01        11.74         3.06         3.25         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56        40.34        70.16        15.62        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.93       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 
       22.98        30.08        16.01        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       14.04        16.04        12.99        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6536 TCGA-D5-6537 
       11.01        12.03        20.19        20.42        17.85         4.50 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       16.14        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       10.26       119.70        49.91         7.50       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       81.37        60.79        98.24        95.18         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 
       13.45         6.18        35.87         1.55        29.59         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       43.07        53.62        51.75        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80         4.11         2.79 
TCGA-QG-A5Z2 
       14.76 

  DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE 
                        0.07                         0.07 
  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 
                       19.79                        20.12 
[1] "0.1 - 140.4 (19.8)" "0.1 - 135.7 (20.1)"
[1] "hr=" "1.2"
D59V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(17P12) MUTATED        35        0       13        53         1
  DEL PEAK 36(17P12) WILD-TYPE      37        1       15        74         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(17P12) MUTATED           1        12         12         32
  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           29       32        12         1
  DEL PEAK 36(17P12) WILD-TYPE          9       10         4         0
D59V3, multiclass
            clus
vv           DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  STAGE I                            35                           37
  STAGE IA                            0                            1
  STAGE II                           13                           15
  STAGE IIA                          53                           74
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                          12                            9
  STAGE IIIA                         12                            1
  STAGE IIIB                         32                           21
  STAGE IIIC                         29                            9
  STAGE IV                           32                           10
  STAGE IVA                          12                            4
  STAGE IVB                           1                            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                           T0+T1  T2  T3  T4
  DEL PEAK 36(17P12) MUTATED       7  40 166  26
  DEL PEAK 36(17P12) WILD-TYPE     4  36 128  22
D59V4, multiclass
       clus
vv      DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  T0+T1                          7                            4
  T2                            40                           36
  T3                           166                          128
  T4                            26                           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   116  67  55
  DEL PEAK 36(17P12) WILD-TYPE 136  34  21
D59V5, multiclass
    clus
vv   DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  N0                        116                          136
  N1                         67                           34
  N2                         55                           21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 36(17P12) MUTATED   168  39   5   1  23
  DEL PEAK 36(17P12) WILD-TYPE 152  11   2   0  22
D59V6, multiclass
     clus
vv    DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  M0                         168                          152
  M1                          39                           11
  M1A                          5                            2
  M1B                          1                            0
  MX                          23                           22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED   107 132
  DEL PEAK 36(17P12) WILD-TYPE  96  95
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED    107  132
  DEL PEAK 36(17P12) WILD-TYPE   96   95
        clus
vv       DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  FEMALE                        107                           96
  MALE                          132                           95
[1] 2 2
[1] FALSE
D59V8, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED   223  14
  DEL PEAK 36(17P12) WILD-TYPE 150  41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED    223   14
  DEL PEAK 36(17P12) WILD-TYPE  150   41
                               clus
vv                              DEL PEAK 36(17P12) MUTATED
  COLON ADENOCARCINOMA                                 223
  COLON MUCINOUS ADENOCARCINOMA                         14
                               clus
vv                              DEL PEAK 36(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   150
  COLON MUCINOUS ADENOCARCINOMA                           41
[1] 2 2
[1] FALSE
D59V9, binary
                              cls
clus                             0   1
  DEL PEAK 36(17P12) MUTATED     3 236
  DEL PEAK 36(17P12) WILD-TYPE   0 191
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 36(17P12) MUTATED      3  236
  DEL PEAK 36(17P12) WILD-TYPE    0  191
     clus
vv    DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  NO                           3                            0
  YES                        236                          191
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 36(17P12) MUTATED   165   1  17  10
  DEL PEAK 36(17P12) WILD-TYPE 140   2   7  14
D59V10, multiclass
    clus
vv   DEL PEAK 36(17P12) MUTATED DEL PEAK 36(17P12) WILD-TYPE
  R0                        165                          140
  R1                          1                            2
  R2                         17                            7
  RX                         10                           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"
D59V11, 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                          23   119
  DEL PEAK 36(17P12) WILD-TYPE                        18    92
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 36(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                23
  WHITE                                                   119
                                  clus
vv                                 DEL PEAK 36(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  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(60) Variable = DEL PEAK 37(17Q24.3) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(17Q24.3) MUTATED    47  16
  DEL PEAK 37(17Q24.3) WILD-TYPE 282  68
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            63                            350 
  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                            16                             68 
$`DEL PEAK 37(17Q24.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 
       37.02        43.76        37.05        32.45        31.63        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 
       25.18        24.16        24.03        12.99        21.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 
        6.05         2.01        50.04        37.05        19.00         0.99 
TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3989 
       37.02        31.07        27.02        24.00        26.01         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01Z 
       34.03        42.02         0.99        32.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 
        2.96        39.98         1.58         1.02         0.20         0.20 
TCGA-AY-A69D TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4751 
        5.52        12.10         3.29         0.26        48.20        27.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 
        5.03        15.02        15.02        14.99         7.92        12.49 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       13.41        11.38        38.20        12.59       140.38        44.32 
TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6809 
        7.76       117.07        13.38        13.45         1.55         1.28 
TCGA-G4-6295 TCGA-NH-A6GA TCGA-QG-A5YV 
        8.35         5.98        26.99 

$`DEL PEAK 37(17Q24.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        15.52        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       16.04        34.65        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       29.16        27.09        24.13         8.38        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        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        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-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-A024 TCGA-AA-A029 
       35.01         1.02        35.01        26.01        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-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-A5EK TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-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-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        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-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-D5-5541 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-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
       24.43       130.65        92.75        49.91        13.32         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        35.97        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        11.11        13.64         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        28.21        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       47.15        52.80         4.11         5.06         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE 
                          0.20                           0.07 
  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 
                         19.00                          20.07 
[1] "0.2 - 140.4 (19.0)" "0.1 - 139.2 (20.1)"
[1] "hr=" "1.5"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(17Q24.3) MUTATED         9        0        5         8         0
  DEL PEAK 37(17Q24.3) WILD-TYPE      63        1       23       119         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(17Q24.3) MUTATED           0         3          4          7
  DEL PEAK 37(17Q24.3) WILD-TYPE         1        18          9         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(17Q24.3) MUTATED           11       10         4         0
  DEL PEAK 37(17Q24.3) WILD-TYPE         27       32        12         1
D60V3, multiclass
            clus
vv           DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                             8                            119
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            4                              9
  STAGE IIIB                            7                             46
  STAGE IIIC                           11                             27
  STAGE IV                             10                             32
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 37(17Q24.3) MUTATED       0  11  44   9
  DEL PEAK 37(17Q24.3) WILD-TYPE    11  65 250  39
D60V4, multiclass
       clus
vv      DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  T0+T1                            0                             11
  T2                              11                             65
  T3                              44                            250
  T4                               9                             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 37(17Q24.3) MUTATED    26  21  17
  DEL PEAK 37(17Q24.3) WILD-TYPE 226  80  59
D60V5, multiclass
    clus
vv   DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  N0                           26                            226
  N1                           21                             80
  N2                           17                             59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 37(17Q24.3) MUTATED    39  11   3   0   9
  DEL PEAK 37(17Q24.3) WILD-TYPE 281  39   4   1  36
D60V6, multiclass
     clus
vv    DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  M0                            39                            281
  M1                            11                             39
  M1A                            3                              4
  M1B                            0                              1
  MX                             9                             36
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED    26  38
  DEL PEAK 37(17Q24.3) WILD-TYPE 177 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED     26   38
  DEL PEAK 37(17Q24.3) WILD-TYPE  177  189
        clus
vv       DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  FEMALE                           26                            177
  MALE                             38                            189
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED    56   8
  DEL PEAK 37(17Q24.3) WILD-TYPE 317  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED     56    8
  DEL PEAK 37(17Q24.3) WILD-TYPE  317   47
                               clus
vv                              DEL PEAK 37(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                    56
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 37(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     317
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(17Q24.3) MUTATED     0  64
  DEL PEAK 37(17Q24.3) WILD-TYPE   3 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(17Q24.3) MUTATED      0   64
  DEL PEAK 37(17Q24.3) WILD-TYPE    3  363
     clus
vv    DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  NO                             0                              3
  YES                           64                            363
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(17Q24.3) MUTATED    40   0   6   4
  DEL PEAK 37(17Q24.3) WILD-TYPE 265   3  18  20
D60V10, multiclass
    clus
vv   DEL PEAK 37(17Q24.3) MUTATED DEL PEAK 37(17Q24.3) WILD-TYPE
  R0                           40                            265
  R1                            0                              3
  R2                            6                             18
  RX                            4                             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"
D60V11, 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                           5    32
  DEL PEAK 37(17Q24.3) WILD-TYPE                        36   179
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 37(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 37(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    36
  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(61) Variable = DEL PEAK 38(18P11.31) MUTATION ANALYSIS
D61V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 38(18P11.31) MUTATED   182  43
  DEL PEAK 38(18P11.31) WILD-TYPE 147  41
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                            225                             188 
  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                             43                              41 
$`DEL PEAK 38(18P11.31) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        24.13        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        37.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       29.00        26.01        14.01        33.99        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       23.01        19.99        13.94        19.99        78.08         6.05 
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-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       12.99        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 
       50.99        13.05        34.06        26.01        24.00         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       13.94        19.00        34.03        17.03        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       14.99        21.99        15.02        15.02        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        26.01         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        5.03        41.00        40.96         4.21         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
        1.02         0.10         0.20         0.43        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
       15.75         5.19         5.52        75.25         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 
       83.80        22.36        65.00        62.79        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        5.23         1.94         2.24         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        0.26         1.35        48.20        21.99         2.01         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02        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-6677 TCGA-CM-6678 TCGA-CM-6679 
       13.02        15.02        11.01        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        13.51        11.51        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       18.25         1.32        17.85        17.13        12.49         7.53 
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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        13.32        12.59       140.38        44.32 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      139.17        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        11.11        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 
       16.24        33.67         1.28         0.53        35.41        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        8.35        82.39        23.51        61.87        55.04        45.11 
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         4.11 
TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06        26.99        17.29 

$`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        23.38        16.04        31.63        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.52         8.38        24.16        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        24.03        36.03         8.05 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       29.00        12.99         0.99        21.01        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       20.98        61.02         6.97        54.02         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       36.03        32.05        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       33.01        26.01        24.00         2.01         2.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       27.02        19.07        27.02        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01         0.99        17.03        34.98         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07        21.37        56.55         0.72         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 
       17.82        50.37        58.39         1.41        32.94        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       49.41         6.77       100.01        11.74         3.19         3.06 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.01         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       23.05        20.02        37.02        26.04        27.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       16.01        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 
       12.99        14.04        12.95        13.05        11.08        19.59 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75         7.92        15.12         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       15.58        12.39        10.13         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        49.91         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      131.51       135.65         7.76         6.12        14.04        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24         8.61        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        43.07        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       51.75        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        35.80        26.17        52.80         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5Z2 
        5.59        14.76 

  DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  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 
                         20.190                          19.625 
[1] "0.1 - 140.4 (20.2)" "0.1 - 135.7 (19.6)"
[1] "hr=" "1.1"
D61V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(18P11.31) MUTATED        35        0       10        62         2
  DEL PEAK 38(18P11.31) WILD-TYPE      37        1       18        65         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(18P11.31) MUTATED           1         9          9         30
  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       31        14         0
  DEL PEAK 38(18P11.31) WILD-TYPE         16       11         2         1
D61V3, multiclass
            clus
vv           DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  STAGE I                               35                              37
  STAGE IA                               0                               1
  STAGE II                              10                              18
  STAGE IIA                             62                              65
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                              9                              12
  STAGE IIIA                             9                               4
  STAGE IIIB                            30                              23
  STAGE IIIC                            22                              16
  STAGE IV                              31                              11
  STAGE IVA                             14                               2
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 38(18P11.31) MUTATED       7  40 158  26
  DEL PEAK 38(18P11.31) WILD-TYPE     4  36 136  22
D61V4, multiclass
       clus
vv      DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  T0+T1                             7                               4
  T2                               40                              36
  T3                              158                             136
  T4                               26                              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   123  64  43
  DEL PEAK 38(18P11.31) WILD-TYPE 129  37  33
D61V5, multiclass
    clus
vv   DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  N0                           123                             129
  N1                            64                              37
  N2                            43                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 38(18P11.31) MUTATED   160  38   7   0  23
  DEL PEAK 38(18P11.31) WILD-TYPE 160  12   0   1  22
D61V6, multiclass
     clus
vv    DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  M0                            160                             160
  M1                             38                              12
  M1A                             7                               0
  M1B                             0                               1
  MX                             23                              22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED   108 123
  DEL PEAK 38(18P11.31) WILD-TYPE  95 104
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED    108  123
  DEL PEAK 38(18P11.31) WILD-TYPE   95  104
        clus
vv       DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  FEMALE                           108                              95
  MALE                             123                             104
[1] 2 2
[1] FALSE
D61V8, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED   222   7
  DEL PEAK 38(18P11.31) WILD-TYPE 151  48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED    222    7
  DEL PEAK 38(18P11.31) WILD-TYPE  151   48
                               clus
vv                              DEL PEAK 38(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                    222
  COLON MUCINOUS ADENOCARCINOMA                             7
                               clus
vv                              DEL PEAK 38(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      151
  COLON MUCINOUS ADENOCARCINOMA                              48
[1] 2 2
[1] FALSE
D61V9, binary
                                 cls
clus                                0   1
  DEL PEAK 38(18P11.31) MUTATED     3 228
  DEL PEAK 38(18P11.31) WILD-TYPE   0 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(18P11.31) MUTATED      3  228
  DEL PEAK 38(18P11.31) WILD-TYPE    0  199
     clus
vv    DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  NO                              3                               0
  YES                           228                             199
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 38(18P11.31) MUTATED   160   0  18  11
  DEL PEAK 38(18P11.31) WILD-TYPE 145   3   6  13
D61V10, multiclass
    clus
vv   DEL PEAK 38(18P11.31) MUTATED DEL PEAK 38(18P11.31) WILD-TYPE
  R0                           160                             145
  R1                             0                               3
  R2                            18                               6
  RX                            11                              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"
D61V11, 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                          22   116
  DEL PEAK 38(18P11.31) WILD-TYPE                        19    95
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 38(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      116
                                  clus
vv                                 DEL PEAK 38(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     19
  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(62) Variable = DEL PEAK 39(18Q12.2) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(18Q12.2) MUTATED   201  50
  DEL PEAK 39(18Q12.2) WILD-TYPE 128  34
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                           251                            162 
  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                            50                             34 
$`DEL PEAK 39(18Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.91        31.63        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        22.52        24.13        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       21.76        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        34.03        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        33.07         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-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       18.05        12.99        24.00         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       24.00        27.02         7.96        19.00        34.03        18.05 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
        0.99        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        40.96         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        0.10         0.76         0.20         0.43         0.46        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4616 
       16.31        15.75         5.19         5.52        75.25         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       29.56         5.23         1.94         2.24         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        0.07         0.26         1.35       102.44        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        1.32        17.85        17.13        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-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-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
        6.12        26.47       119.93       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        11.11        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       16.24         1.28         0.53        35.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       39.42        35.93        36.72        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX 
       47.15         4.11         5.06        26.99        17.29 

$`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        23.38        33.53        22.09        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 
        1.02        13.02         1.02         8.05        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       47.05        11.01         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        32.05        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       26.01        24.00         2.01        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       27.02         0.99        34.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R 
        1.02        35.01        35.01        39.06        51.98        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       39.98        18.05         0.07        21.37        56.55         0.72 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95         0.20        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 
       50.37        58.39         1.41         5.65        32.94        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         3.19         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       13.05        20.42        17.75         7.92        15.12         4.50 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       16.14        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C 
       10.26       119.70       135.65         7.76        14.04        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       35.97        60.79        98.24        13.64         6.18        35.87 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       33.67        19.43       107.67        74.56        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       51.75        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
       26.17        52.80         2.79         5.98         5.59        14.76 

  DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                         19.99                          19.84 
[1] "0.1 - 140.4 (20.0)" "0.1 - 135.7 (19.8)"
[1] "hr=" "1.1"
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18Q12.2) MUTATED        37        0       15        66         2
  DEL PEAK 39(18Q12.2) WILD-TYPE      35        1       13        61         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q12.2) MUTATED           1        11         12         34
  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           26       34        12         0
  DEL PEAK 39(18Q12.2) WILD-TYPE         12        8         4         1
D62V3, multiclass
            clus
vv           DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  STAGE I                              37                             35
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            66                             61
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           12                              1
  STAGE IIIB                           34                             19
  STAGE IIIC                           26                             12
  STAGE IV                             34                              8
  STAGE IVA                            12                              4
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 39(18Q12.2) MUTATED       6  44 181  26
  DEL PEAK 39(18Q12.2) WILD-TYPE     5  32 113  22
D62V4, multiclass
       clus
vv      DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  T0+T1                            6                              5
  T2                              44                             32
  T3                             181                            113
  T4                              26                             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   133  70  53
  DEL PEAK 39(18Q12.2) WILD-TYPE 119  31  23
D62V5, multiclass
    clus
vv   DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  N0                          133                            119
  N1                           70                             31
  N2                           53                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 39(18Q12.2) MUTATED   185  40   6   0  23
  DEL PEAK 39(18Q12.2) WILD-TYPE 135  10   1   1  22
D62V6, multiclass
     clus
vv    DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  M0                           185                            135
  M1                            40                             10
  M1A                            6                              1
  M1B                            0                              1
  MX                            23                             22
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED   116 141
  DEL PEAK 39(18Q12.2) WILD-TYPE  87  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED    116  141
  DEL PEAK 39(18Q12.2) WILD-TYPE   87   86
        clus
vv       DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  FEMALE                          116                             87
  MALE                            141                             86
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED   245  11
  DEL PEAK 39(18Q12.2) WILD-TYPE 128  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED    245   11
  DEL PEAK 39(18Q12.2) WILD-TYPE  128   44
                               clus
vv                              DEL PEAK 39(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                   245
  COLON MUCINOUS ADENOCARCINOMA                           11
                               clus
vv                              DEL PEAK 39(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     128
  COLON MUCINOUS ADENOCARCINOMA                             44
[1] 2 2
[1] FALSE
D62V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q12.2) MUTATED     3 254
  DEL PEAK 39(18Q12.2) WILD-TYPE   0 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q12.2) MUTATED      3  254
  DEL PEAK 39(18Q12.2) WILD-TYPE    0  173
     clus
vv    DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  NO                             3                              0
  YES                          254                            173
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(18Q12.2) MUTATED   180   1  18  11
  DEL PEAK 39(18Q12.2) WILD-TYPE 125   2   6  13
D62V10, multiclass
    clus
vv   DEL PEAK 39(18Q12.2) MUTATED DEL PEAK 39(18Q12.2) WILD-TYPE
  R0                          180                            125
  R1                            1                              2
  R2                           18                              6
  RX                           11                             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"
D62V11, 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                          22   131
  DEL PEAK 39(18Q12.2) WILD-TYPE                        19    80
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 39(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     131
                                  clus
vv                                 DEL PEAK 39(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                        80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 40(18Q21.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(18Q21.2) MUTATED   211  54
  DEL PEAK 40(18Q21.2) WILD-TYPE 118  30
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                           265                            148 
  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                            54                             30 
$`DEL PEAK 40(18Q21.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.39        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-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-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       15.02         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.99        33.07         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        34.03        18.05        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K 
       21.99        15.02        15.02         0.99        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
        1.02        33.04        26.01        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
        2.01         5.03         0.92        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         1.58         1.02         0.10         0.20         0.43 
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         5.19         5.52 
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-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.26         1.35       102.44        48.20        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       16.04        21.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
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-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25         1.32        17.85        17.13        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        1.28         0.53        35.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 
       39.42        35.93        36.72        36.00        26.04        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.98        26.99 
TCGA-QG-A5YX 
       17.29 

$`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        23.38        33.53        22.06         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
        1.02         8.05        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       20.98         6.97         0.92        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        1.02        17.98        15.95        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        17.03         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       39.06        51.98        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       21.37        56.55         0.72         0.76         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
        0.95         0.20        21.44        17.82        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 
        1.41        32.94        49.41         6.77       100.01         3.06 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        3.25         0.33         0.10        17.56        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        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        26.04        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       12.95        20.42         7.92        15.12         4.50        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-A28G TCGA-F4-6463 
      119.70       135.65         7.76        81.37        60.79        13.64 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 
        6.18        35.87        19.43       107.67        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       51.75        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 
       52.80         2.79         5.59        14.76 

  DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  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 
                        20.190                         19.545 
[1] "0.1 - 140.4 (20.2)" "0.1 - 135.7 (19.5)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18Q21.2) MUTATED        39        0       16        68         2
  DEL PEAK 40(18Q21.2) WILD-TYPE      33        1       12        59         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18Q21.2) MUTATED           1        11         12         36
  DEL PEAK 40(18Q21.2) WILD-TYPE         0        10          1         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18Q21.2) MUTATED           30       36        13         1
  DEL PEAK 40(18Q21.2) WILD-TYPE          8        6         3         0
D63V3, multiclass
            clus
vv           DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  STAGE I                              39                             33
  STAGE IA                              0                              1
  STAGE II                             16                             12
  STAGE IIA                            68                             59
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           12                              1
  STAGE IIIB                           36                             17
  STAGE IIIC                           30                              8
  STAGE IV                             36                              6
  STAGE IVA                            13                              3
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 40(18Q21.2) MUTATED       7  45 189  30
  DEL PEAK 40(18Q21.2) WILD-TYPE     4  31 105  18
D63V4, multiclass
       clus
vv      DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  T0+T1                            7                              4
  T2                              45                             31
  T3                             189                            105
  T4                              30                             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   138  73  59
  DEL PEAK 40(18Q21.2) WILD-TYPE 114  28  17
D63V5, multiclass
    clus
vv   DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  N0                          138                            114
  N1                           73                             28
  N2                           59                             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 40(18Q21.2) MUTATED   193  43   6   1  26
  DEL PEAK 40(18Q21.2) WILD-TYPE 127   7   1   0  19
D63V6, multiclass
     clus
vv    DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  M0                           193                            127
  M1                            43                              7
  M1A                            6                              1
  M1B                            1                              0
  MX                            26                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED   119 152
  DEL PEAK 40(18Q21.2) WILD-TYPE  84  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED    119  152
  DEL PEAK 40(18Q21.2) WILD-TYPE   84   75
        clus
vv       DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  FEMALE                          119                             84
  MALE                            152                             75
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED   256  14
  DEL PEAK 40(18Q21.2) WILD-TYPE 117  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED    256   14
  DEL PEAK 40(18Q21.2) WILD-TYPE  117   41
                               clus
vv                              DEL PEAK 40(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   256
  COLON MUCINOUS ADENOCARCINOMA                           14
                               clus
vv                              DEL PEAK 40(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     117
  COLON MUCINOUS ADENOCARCINOMA                             41
[1] 2 2
[1] FALSE
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(18Q21.2) MUTATED     3 268
  DEL PEAK 40(18Q21.2) WILD-TYPE   0 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(18Q21.2) MUTATED      3  268
  DEL PEAK 40(18Q21.2) WILD-TYPE    0  159
     clus
vv    DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  NO                             3                              0
  YES                          268                            159
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(18Q21.2) MUTATED   188   1  18  11
  DEL PEAK 40(18Q21.2) WILD-TYPE 117   2   6  13
D63V10, multiclass
    clus
vv   DEL PEAK 40(18Q21.2) MUTATED DEL PEAK 40(18Q21.2) WILD-TYPE
  R0                          188                            117
  R1                            1                              2
  R2                           18                              6
  RX                           11                             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"
D63V11, 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                          25   141
  DEL PEAK 40(18Q21.2) WILD-TYPE                        16    70
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 40(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     141
                                  clus
vv                                 DEL PEAK 40(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  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(64) Variable = DEL PEAK 41(18Q22.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q22.1) MUTATED   211  54
  DEL PEAK 41(18Q22.1) WILD-TYPE 118  30
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                           265                            148 
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                            54                             30 
$`DEL PEAK 41(18Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.39        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-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-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       15.02         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.99        33.07         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-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        13.94        19.00        34.03        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L 
        0.43         0.46        14.50        16.31        15.75         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        5.52        75.25         5.65         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        61.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.07         0.26         1.35        48.20        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       16.04        21.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
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-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25         1.32        15.12        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       33.67         1.28         0.53        35.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       82.39        23.51        74.56        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       45.11        39.42        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.98        26.99 
TCGA-QG-A5YX 
       17.29 

$`DEL PEAK 41(18Q22.1) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       46.65        23.38        33.53        22.06         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
        1.02         8.05        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       20.98         6.97         0.92        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3877 
        1.02        17.98        15.95        36.03        32.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       19.07        27.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       17.03         4.01        27.02         0.99        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       31.00        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       51.98        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.72         0.76         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        21.44        17.82        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 
       32.94        49.41         6.77       100.01         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        26.04        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       12.95        20.42         7.92         4.50        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 
      135.65         7.76        81.37        60.79        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       35.87        19.43       107.67        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 
       52.80         2.79         5.59        14.76 

  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE 
                         19.99                          19.84 
[1] "0.1 - 140.4 (20.0)" "0.1 - 135.7 (19.8)"
[1] "hr=" "1"  
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(18Q22.1) MUTATED        39        0       17        68         2
  DEL PEAK 41(18Q22.1) WILD-TYPE      33        1       11        59         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q22.1) MUTATED           1        11         11         36
  DEL PEAK 41(18Q22.1) WILD-TYPE         0        10          2         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(18Q22.1) MUTATED           30       36        13         1
  DEL PEAK 41(18Q22.1) WILD-TYPE          8        6         3         0
D64V3, multiclass
            clus
vv           DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  STAGE I                              39                             33
  STAGE IA                              0                              1
  STAGE II                             17                             11
  STAGE IIA                            68                             59
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           11                              2
  STAGE IIIB                           36                             17
  STAGE IIIC                           30                              8
  STAGE IV                             36                              6
  STAGE IVA                            13                              3
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 41(18Q22.1) MUTATED       7  45 189  30
  DEL PEAK 41(18Q22.1) WILD-TYPE     4  31 105  18
D64V4, multiclass
       clus
vv      DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  T0+T1                            7                              4
  T2                              45                             31
  T3                             189                            105
  T4                              30                             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 41(18Q22.1) MUTATED   139  72  59
  DEL PEAK 41(18Q22.1) WILD-TYPE 113  29  17
D64V5, multiclass
    clus
vv   DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  N0                          139                            113
  N1                           72                             29
  N2                           59                             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 41(18Q22.1) MUTATED   193  43   6   1  26
  DEL PEAK 41(18Q22.1) WILD-TYPE 127   7   1   0  19
D64V6, multiclass
     clus
vv    DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  M0                           193                            127
  M1                            43                              7
  M1A                            6                              1
  M1B                            1                              0
  MX                            26                             19
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.1) MUTATED   119 152
  DEL PEAK 41(18Q22.1) WILD-TYPE  84  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.1) MUTATED    119  152
  DEL PEAK 41(18Q22.1) WILD-TYPE   84   75
        clus
vv       DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  FEMALE                          119                             84
  MALE                            152                             75
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.1) MUTATED   257  13
  DEL PEAK 41(18Q22.1) WILD-TYPE 116  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.1) MUTATED    257   13
  DEL PEAK 41(18Q22.1) WILD-TYPE  116   42
                               clus
vv                              DEL PEAK 41(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   257
  COLON MUCINOUS ADENOCARCINOMA                           13
                               clus
vv                              DEL PEAK 41(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     116
  COLON MUCINOUS ADENOCARCINOMA                             42
[1] 2 2
[1] FALSE
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q22.1) MUTATED     3 268
  DEL PEAK 41(18Q22.1) WILD-TYPE   0 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q22.1) MUTATED      3  268
  DEL PEAK 41(18Q22.1) WILD-TYPE    0  159
     clus
vv    DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  NO                             3                              0
  YES                          268                            159
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(18Q22.1) MUTATED   187   1  18  12
  DEL PEAK 41(18Q22.1) WILD-TYPE 118   2   6  12
D64V10, multiclass
    clus
vv   DEL PEAK 41(18Q22.1) MUTATED DEL PEAK 41(18Q22.1) WILD-TYPE
  R0                          187                            118
  R1                            1                              2
  R2                           18                              6
  RX                           12                             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"
D64V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(18Q22.1) MUTATED                                  1     6
  DEL PEAK 41(18Q22.1) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q22.1) MUTATED                          25   140
  DEL PEAK 41(18Q22.1) WILD-TYPE                        16    71
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     140
                                  clus
vv                                 DEL PEAK 41(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                        71
[1] 4 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 42(19P13.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(19P13.3) MUTATED    44  13
  DEL PEAK 42(19P13.3) WILD-TYPE 285  71
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                            57                            356 
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                            13                             71 
$`DEL PEAK 42(19P13.3) MUTATED`
TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3519 
       34.65        25.08        21.76        61.84        58.03         9.07 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       26.01        12.99        13.02        23.01        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3860 TCGA-AA-3866 
        2.01        36.00        36.95        37.02        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 
       24.03        27.02        24.00         2.01        50.99        24.00 
TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F 
       27.02         0.99        12.00        33.04        26.01        39.98 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4616 
       41.00         1.02         0.20        16.31         0.20         5.13 
TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6169 TCGA-CM-6675 
       65.00         3.29       102.44        48.20        13.02        13.05 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6541 
       10.06        14.99        20.19         1.32         4.50        15.58 
TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-F4-6461 TCGA-F4-6808 
       10.13       119.70        44.32       131.51        11.11        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 
        8.35        82.39        36.00 

$`DEL PEAK 42(19P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13         8.38        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
        3.02         1.02        37.05         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        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-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-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-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-3982 
       16.08        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        15.02        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-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-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-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.58         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.43         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
       15.75        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-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        21.01         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-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 
        7.92        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         1.28         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        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
        4.11         5.06         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE 
                         23.01                          19.51 
[1] "0.2 - 131.5 (23.0)" "0.1 - 140.4 (19.5)"
[1] "hr=" "1"  
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(19P13.3) MUTATED         8        0        1        10         0
  DEL PEAK 42(19P13.3) WILD-TYPE      64        1       27       117         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(19P13.3) MUTATED           0         4          4          4
  DEL PEAK 42(19P13.3) WILD-TYPE         1        17          9         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(19P13.3) MUTATED           12       10         3         1
  DEL PEAK 42(19P13.3) WILD-TYPE         26       32        13         0
D65V3, multiclass
            clus
vv           DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  STAGE I                               8                             64
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            10                            117
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            4                              9
  STAGE IIIB                            4                             49
  STAGE IIIC                           12                             26
  STAGE IV                             10                             32
  STAGE IVA                             3                             13
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 42(19P13.3) MUTATED       1   9  42   7
  DEL PEAK 42(19P13.3) WILD-TYPE    10  67 252  41
D65V4, multiclass
       clus
vv      DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  T0+T1                            1                             10
  T2                               9                             67
  T3                              42                            252
  T4                               7                             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 42(19P13.3) MUTATED    22  15  22
  DEL PEAK 42(19P13.3) WILD-TYPE 230  86  54
D65V5, multiclass
    clus
vv   DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  N0                           22                            230
  N1                           15                             86
  N2                           22                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 42(19P13.3) MUTATED    37  11   2   1   7
  DEL PEAK 42(19P13.3) WILD-TYPE 283  39   5   0  38
D65V6, multiclass
     clus
vv    DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  M0                            37                            283
  M1                            11                             39
  M1A                            2                              5
  M1B                            1                              0
  MX                             7                             38
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(19P13.3) MUTATED    25  34
  DEL PEAK 42(19P13.3) WILD-TYPE 178 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(19P13.3) MUTATED     25   34
  DEL PEAK 42(19P13.3) WILD-TYPE  178  193
        clus
vv       DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  FEMALE                           25                            178
  MALE                             34                            193
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(19P13.3) MUTATED    54   4
  DEL PEAK 42(19P13.3) WILD-TYPE 319  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(19P13.3) MUTATED     54    4
  DEL PEAK 42(19P13.3) WILD-TYPE  319   51
                               clus
vv                              DEL PEAK 42(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                    54
  COLON MUCINOUS ADENOCARCINOMA                            4
                               clus
vv                              DEL PEAK 42(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     319
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(19P13.3) MUTATED     1  58
  DEL PEAK 42(19P13.3) WILD-TYPE   2 369
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(19P13.3) MUTATED      1   58
  DEL PEAK 42(19P13.3) WILD-TYPE    2  369
     clus
vv    DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  NO                             1                              2
  YES                           58                            369
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(19P13.3) MUTATED    37   1   7   3
  DEL PEAK 42(19P13.3) WILD-TYPE 268   2  17  21
D65V10, multiclass
    clus
vv   DEL PEAK 42(19P13.3) MUTATED DEL PEAK 42(19P13.3) WILD-TYPE
  R0                           37                            268
  R1                            1                              2
  R2                            7                             17
  RX                            3                             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"
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(19P13.3) MUTATED                                  0     1
  DEL PEAK 42(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(19P13.3) MUTATED                           4    25
  DEL PEAK 42(19P13.3) WILD-TYPE                        37   186
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 42(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK 42(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    37
  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(66) Variable = DEL PEAK 43(20P12.1) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(20P12.1) MUTATED    90  27
  DEL PEAK 43(20P12.1) WILD-TYPE 239  57
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                           117                            296 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                            27                             57 
$`DEL PEAK 43(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5660 
       17.79        42.28        15.52        34.65        14.53        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 
       23.61        32.71        29.16        24.13        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3496 TCGA-AA-3510 
       24.39        20.12        20.28        52.44         1.02        63.98 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       38.99         9.07        34.03        26.01        12.99         0.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3715 
       24.00        13.94        78.08         5.98        85.05         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3848 
        0.99        35.05        25.02         1.02        36.95         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 
       32.05        31.07        53.00        24.03         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       34.03         2.01        27.02        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z 
       42.02        32.02        12.00        31.00         1.02        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6964 
        2.96        39.98        40.96        21.37         1.58         0.76 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        0.20        15.75        75.25         5.23        11.74         1.94 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
      102.44        21.99         2.01         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
       22.03        30.08        16.01        29.03        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 
       11.51         1.32         7.92        15.12         7.53        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A 
       92.75        49.91        13.32        44.32       131.51        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      119.93        35.97         8.61        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 
        1.28         0.53        28.21         8.35        23.51        36.72 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50V 
       26.43        46.75         5.06 

$`DEL PEAK 43(20P12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        24.16        20.61        24.69        23.87        19.66 
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         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        58.03         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 
        8.05        19.07        19.07        29.00        29.00        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 
        5.03        26.99        19.04         0.99        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       38.99        37.02        14.93        17.03        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       24.00        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-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-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-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        15.02         0.99        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.02         0.10         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        48.20        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       26.04        29.06        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       21.99        14.99        14.04        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        14.99        19.59        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04         9.44        11.64        12.00       119.70        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       14.04        81.37        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-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        1.55        16.31        35.41        19.43       107.67        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
       52.80         4.11         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE 
                         21.37                          19.51 
[1] "0.2 - 131.5 (21.4)" "0.1 - 140.4 (19.5)"
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(20P12.1) MUTATED        15        0       10        33         1
  DEL PEAK 43(20P12.1) WILD-TYPE      57        1       18        94         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(20P12.1) MUTATED           1         5          3         23
  DEL PEAK 43(20P12.1) WILD-TYPE         0        16         10         30
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(20P12.1) MUTATED           13       10         5         0
  DEL PEAK 43(20P12.1) WILD-TYPE         25       32        11         1
D66V3, multiclass
            clus
vv           DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  STAGE I                              15                             57
  STAGE IA                              0                              1
  STAGE II                             10                             18
  STAGE IIA                            33                             94
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             5                             16
  STAGE IIIA                            3                             10
  STAGE IIIB                           23                             30
  STAGE IIIC                           13                             25
  STAGE IV                             10                             32
  STAGE IVA                             5                             11
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 43(20P12.1) MUTATED       2  16  89  14
  DEL PEAK 43(20P12.1) WILD-TYPE     9  60 205  34
D66V4, multiclass
       clus
vv      DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  T0+T1                            2                              9
  T2                              16                             60
  T3                              89                            205
  T4                              14                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 43(20P12.1) MUTATED    64  35  22
  DEL PEAK 43(20P12.1) WILD-TYPE 188  66  54
D66V5, multiclass
    clus
vv   DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  N0                           64                            188
  N1                           35                             66
  N2                           22                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 43(20P12.1) MUTATED    95  13   2   0  10
  DEL PEAK 43(20P12.1) WILD-TYPE 225  37   5   1  35
D66V6, multiclass
     clus
vv    DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  M0                            95                            225
  M1                            13                             37
  M1A                            2                              5
  M1B                            0                              1
  MX                            10                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(20P12.1) MUTATED    59  62
  DEL PEAK 43(20P12.1) WILD-TYPE 144 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(20P12.1) MUTATED     59   62
  DEL PEAK 43(20P12.1) WILD-TYPE  144  165
        clus
vv       DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  FEMALE                           59                            144
  MALE                             62                            165
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(20P12.1) MUTATED   108  13
  DEL PEAK 43(20P12.1) WILD-TYPE 265  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(20P12.1) MUTATED    108   13
  DEL PEAK 43(20P12.1) WILD-TYPE  265   42
                               clus
vv                              DEL PEAK 43(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                   108
  COLON MUCINOUS ADENOCARCINOMA                           13
                               clus
vv                              DEL PEAK 43(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  COLON MUCINOUS ADENOCARCINOMA                             42
[1] 2 2
[1] FALSE
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(20P12.1) MUTATED     0 121
  DEL PEAK 43(20P12.1) WILD-TYPE   3 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(20P12.1) MUTATED      0  121
  DEL PEAK 43(20P12.1) WILD-TYPE    3  306
     clus
vv    DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  NO                             0                              3
  YES                          121                            306
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(20P12.1) MUTATED    85   0   4   3
  DEL PEAK 43(20P12.1) WILD-TYPE 220   3  20  21
D66V10, multiclass
    clus
vv   DEL PEAK 43(20P12.1) MUTATED DEL PEAK 43(20P12.1) WILD-TYPE
  R0                           85                            220
  R1                            0                              3
  R2                            4                             20
  RX                            3                             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"
D66V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(20P12.1) MUTATED                                  0     0
  DEL PEAK 43(20P12.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(20P12.1) MUTATED                           8    68
  DEL PEAK 43(20P12.1) WILD-TYPE                        33   143
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 43(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      68
                                  clus
vv                                 DEL PEAK 43(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    33
  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(67) Variable = DEL PEAK 44(20P12.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(20P12.1) MUTATED    90  27
  DEL PEAK 44(20P12.1) WILD-TYPE 239  57
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                           117                            296 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                            27                             57 
$`DEL PEAK 44(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5660 
       17.79        42.28        15.52        34.65        14.53        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 
       23.61        32.71        29.16        24.13        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3496 TCGA-AA-3510 
       24.39        20.12        20.28        52.44         1.02        63.98 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       38.99         9.07        34.03        26.01        12.99         0.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3715 
       24.00        13.94        78.08         5.98        85.05         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3848 
        0.99        35.05        25.02         1.02        36.95         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 
       32.05        31.07        53.00        24.03         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       34.03         2.01        27.02        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z 
       42.02        32.02        12.00        31.00         1.02        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6964 
        2.96        39.98        40.96        21.37         1.58         0.76 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        0.20        15.75        75.25         5.23        11.74         1.94 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
      102.44        21.99         2.01         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
       22.03        30.08        16.01        29.03        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 
       11.51         1.32         7.92        15.12         7.53        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A 
       92.75        49.91        13.32        44.32       131.51        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      119.93        35.97         8.61        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 
        1.28         0.53        28.21         8.35        23.51        36.72 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50V 
       26.43        46.75         5.06 

$`DEL PEAK 44(20P12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        24.16        20.61        24.69        23.87        19.66 
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         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        58.03         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 
        8.05        19.07        19.07        29.00        29.00        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 
        5.03        26.99        19.04         0.99        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       38.99        37.02        14.93        17.03        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       24.00        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-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-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-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        15.02         0.99        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.02         0.10         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        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-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        48.20        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       26.04        29.06        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       21.99        14.99        14.04        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        14.99        19.59        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04         9.44        11.64        12.00       119.70        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       14.04        81.37        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-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        1.55        16.31        35.41        19.43       107.67        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
       52.80         4.11         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE 
                         21.37                          19.51 
[1] "0.2 - 131.5 (21.4)" "0.1 - 140.4 (19.5)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 44(20P12.1) MUTATED        15        0       10        33         1
  DEL PEAK 44(20P12.1) WILD-TYPE      57        1       18        94         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(20P12.1) MUTATED           1         5          3         23
  DEL PEAK 44(20P12.1) WILD-TYPE         0        16         10         30
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(20P12.1) MUTATED           13       10         5         0
  DEL PEAK 44(20P12.1) WILD-TYPE         25       32        11         1
D67V3, multiclass
            clus
vv           DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  STAGE I                              15                             57
  STAGE IA                              0                              1
  STAGE II                             10                             18
  STAGE IIA                            33                             94
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             5                             16
  STAGE IIIA                            3                             10
  STAGE IIIB                           23                             30
  STAGE IIIC                           13                             25
  STAGE IV                             10                             32
  STAGE IVA                             5                             11
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 44(20P12.1) MUTATED       2  16  89  14
  DEL PEAK 44(20P12.1) WILD-TYPE     9  60 205  34
D67V4, multiclass
       clus
vv      DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  T0+T1                            2                              9
  T2                              16                             60
  T3                              89                            205
  T4                              14                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 44(20P12.1) MUTATED    64  35  22
  DEL PEAK 44(20P12.1) WILD-TYPE 188  66  54
D67V5, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  N0                           64                            188
  N1                           35                             66
  N2                           22                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 44(20P12.1) MUTATED    95  13   2   0  10
  DEL PEAK 44(20P12.1) WILD-TYPE 225  37   5   1  35
D67V6, multiclass
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  M0                            95                            225
  M1                            13                             37
  M1A                            2                              5
  M1B                            0                              1
  MX                            10                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED    59  62
  DEL PEAK 44(20P12.1) WILD-TYPE 144 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED     59   62
  DEL PEAK 44(20P12.1) WILD-TYPE  144  165
        clus
vv       DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  FEMALE                           59                            144
  MALE                             62                            165
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED   108  13
  DEL PEAK 44(20P12.1) WILD-TYPE 265  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED    108   13
  DEL PEAK 44(20P12.1) WILD-TYPE  265   42
                               clus
vv                              DEL PEAK 44(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                   108
  COLON MUCINOUS ADENOCARCINOMA                           13
                               clus
vv                              DEL PEAK 44(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  COLON MUCINOUS ADENOCARCINOMA                             42
[1] 2 2
[1] FALSE
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(20P12.1) MUTATED     0 121
  DEL PEAK 44(20P12.1) WILD-TYPE   3 306
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(20P12.1) MUTATED      0  121
  DEL PEAK 44(20P12.1) WILD-TYPE    3  306
     clus
vv    DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  NO                             0                              3
  YES                          121                            306
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(20P12.1) MUTATED    85   0   4   3
  DEL PEAK 44(20P12.1) WILD-TYPE 220   3  20  21
D67V10, multiclass
    clus
vv   DEL PEAK 44(20P12.1) MUTATED DEL PEAK 44(20P12.1) WILD-TYPE
  R0                           85                            220
  R1                            0                              3
  R2                            4                             20
  RX                            3                             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"
D67V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(20P12.1) MUTATED                                  0     0
  DEL PEAK 44(20P12.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(20P12.1) MUTATED                           8    68
  DEL PEAK 44(20P12.1) WILD-TYPE                        33   143
D67V12, multiclass
                                  clus
vv                                 DEL PEAK 44(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      68
                                  clus
vv                                 DEL PEAK 44(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    33
  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(68) Variable = DEL PEAK 45(21Q11.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q11.2) MUTATED   103  26
  DEL PEAK 45(21Q11.2) WILD-TYPE 226  58
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           129                            284 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                            26                             58 
$`DEL PEAK 45(21Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 
       37.02        43.76        42.28        37.05        14.53        30.44 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 
       38.99         9.07        19.07        19.07        34.03        26.01 
TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3685 
       14.01        13.02        23.01        19.99        78.08        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       19.00        36.00         0.99        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       18.05        24.00        20.98         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C 
       13.94        17.03        27.02        42.02        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        0.99        32.02        31.00        51.98        39.98         2.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
        0.92        41.00         0.79         1.02         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 
       14.50        16.31         0.95         5.52         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         3.19         2.24         2.14 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
        3.29         0.26        48.20        21.99         2.01        20.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        8.02        27.02        13.02        22.03        16.01         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        29.03        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       14.99        17.75         1.32        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
        9.04        13.41        11.38        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        7.50       131.51        26.47        13.38        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       29.59        16.24        33.67         0.53        35.41         8.35 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.72        36.00        26.43        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
        4.11         5.98        26.99 

$`DEL PEAK 45(21Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
        5.06        46.65        43.43        23.38        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       33.53        23.61        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 
        8.38        25.08        25.18        24.16        24.69        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       19.66        16.24        24.92        52.44         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
        8.05        29.00        29.00        12.99         0.99        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       21.01        24.00        17.95        29.95        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95        17.03        33.07        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         1.58         0.10         0.76         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         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-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-5255 TCGA-CA-5796 TCGA-CA-6715 
      100.01        11.74         1.94         3.06         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-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.01         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 
       23.05        37.02         8.02        26.04        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       30.08        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         7.92        15.12        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6927 
       12.49        16.14        15.58         7.53        12.39         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-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
       38.20       130.65        92.75        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 
       11.11        13.64        13.45         6.18        16.31         1.28 
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-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       45.11        39.42        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         5.06         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        18.050                         20.995 
[1] "0.2 - 140.4 (18.1)" "0.1 - 139.2 (21.0)"
[1] "hr=" "1.2"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 45(21Q11.2) MUTATED        22        0        8        34         1
  DEL PEAK 45(21Q11.2) WILD-TYPE      50        1       20        93         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(21Q11.2) MUTATED           0         4          6         15
  DEL PEAK 45(21Q11.2) WILD-TYPE         1        17          7         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 45(21Q11.2) MUTATED           17       20         4         0
  DEL PEAK 45(21Q11.2) WILD-TYPE         21       22        12         1
D68V3, multiclass
            clus
vv           DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  STAGE I                              22                             50
  STAGE IA                              0                              1
  STAGE II                              8                             20
  STAGE IIA                            34                             93
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            6                              7
  STAGE IIIB                           15                             38
  STAGE IIIC                           17                             21
  STAGE IV                             20                             22
  STAGE IVA                             4                             12
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 45(21Q11.2) MUTATED       6  22  90  17
  DEL PEAK 45(21Q11.2) WILD-TYPE     5  54 204  31
D68V4, multiclass
       clus
vv      DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  T0+T1                            6                              5
  T2                              22                             54
  T3                              90                            204
  T4                              17                             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 45(21Q11.2) MUTATED    69  32  34
  DEL PEAK 45(21Q11.2) WILD-TYPE 183  69  42
D68V5, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  N0                           69                            183
  N1                           32                             69
  N2                           34                             42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 45(21Q11.2) MUTATED    91  21   3   0  19
  DEL PEAK 45(21Q11.2) WILD-TYPE 229  29   4   1  26
D68V6, multiclass
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  M0                            91                            229
  M1                            21                             29
  M1A                            3                              4
  M1B                            0                              1
  MX                            19                             26
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    62  73
  DEL PEAK 45(21Q11.2) WILD-TYPE 141 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     62   73
  DEL PEAK 45(21Q11.2) WILD-TYPE  141  154
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  FEMALE                           62                            141
  MALE                             73                            154
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   125   8
  DEL PEAK 45(21Q11.2) WILD-TYPE 248  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    125    8
  DEL PEAK 45(21Q11.2) WILD-TYPE  248   47
                               clus
vv                              DEL PEAK 45(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   125
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 45(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     248
  COLON MUCINOUS ADENOCARCINOMA                             47
[1] 2 2
[1] FALSE
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED     2 133
  DEL PEAK 45(21Q11.2) WILD-TYPE   1 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED      2  133
  DEL PEAK 45(21Q11.2) WILD-TYPE    1  294
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  NO                             2                              1
  YES                          133                            294
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(21Q11.2) MUTATED    92   1  10   7
  DEL PEAK 45(21Q11.2) WILD-TYPE 213   2  14  17
D68V10, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  R0                           92                            213
  R1                            1                              2
  R2                           10                             14
  RX                            7                             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"
D68V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(21Q11.2) MUTATED                                  1     4
  DEL PEAK 45(21Q11.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(21Q11.2) MUTATED                          13    66
  DEL PEAK 45(21Q11.2) WILD-TYPE                        28   145
D68V12, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 45(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = DEL PEAK 46(22Q13.32) MUTATION ANALYSIS
D69V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(22Q13.32) MUTATED   114  33
  DEL PEAK 46(22Q13.32) WILD-TYPE 215  51
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            147                             266 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                             33                              51 
$`DEL PEAK 46(22Q13.32) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       15.52        34.65        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       29.19        23.61        22.52        20.61        21.76        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         9.63         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       24.03        37.05        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 
       21.01        13.02        19.99        13.94         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 
       50.04         5.98        37.05        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 
       29.98        18.05         2.01        12.99         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 
       21.99        50.99        13.05        26.01         7.96        13.94 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W 
       15.02        33.04        26.01        37.02        39.98        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       40.96         1.58         1.02         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 TCGA-AZ-4614 
       16.31        15.75         0.20         5.52         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6748 
        2.24         3.06         0.26         1.35        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
        8.02         8.02        29.06        30.08         5.03        15.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        14.99        13.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.19         1.32         7.92        15.12        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 
        7.53        12.43        13.41        11.38       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       12.59       140.38        44.32       131.51         6.12        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 
       13.38         1.55        16.24         1.28         8.35        82.39 
TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       45.11        36.72        36.00        91.79        46.75         4.11 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
        5.06         5.98        26.99 

$`DEL PEAK 46(22Q13.32) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5661 
       37.05        37.25        16.04        32.45        32.91        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        24.16        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 
       20.12        19.66        20.28        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3524 
       58.03        63.98         1.02        13.02         1.02        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 
        8.05        19.07        19.07        34.03        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       14.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 
        0.92        47.05        47.01        15.02        11.01        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        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-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       36.03        53.00        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       24.00        20.98        34.03        16.08        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.79         0.72         0.10         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.95        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25        50.37        58.39        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       11.74         2.14         3.25         3.29         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       20.02        37.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-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-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       11.08        12.03        12.26        19.59        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       17.75        18.25         4.50        17.13        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        49.91         7.50       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       14.04        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-F4-6808 TCGA-F4-6854 
        6.18        35.87        16.31        29.59        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6311 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         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 
       17.29        14.76 

  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         16.310                          20.995 
[1] "0.2 - 140.4 (16.3)" "0.1 - 139.2 (21.0)"
[1] "hr=" "1.4"
D69V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 46(22Q13.32) MUTATED        18        0        7        38         1
  DEL PEAK 46(22Q13.32) WILD-TYPE      54        1       21        89         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(22Q13.32) MUTATED           0         7          8         16
  DEL PEAK 46(22Q13.32) WILD-TYPE         1        14          5         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(22Q13.32) MUTATED           20       24         7         0
  DEL PEAK 46(22Q13.32) WILD-TYPE         18       18         9         1
D69V3, multiclass
            clus
vv           DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  STAGE I                               18                              54
  STAGE IA                               0                               1
  STAGE II                               7                              21
  STAGE IIA                             38                              89
  STAGE IIB                              1                               7
  STAGE IIC                              0                               1
  STAGE III                              7                              14
  STAGE IIIA                             8                               5
  STAGE IIIB                            16                              37
  STAGE IIIC                            20                              18
  STAGE IV                              24                              18
  STAGE IVA                              7                               9
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 46(22Q13.32) MUTATED       3  23 104  20
  DEL PEAK 46(22Q13.32) WILD-TYPE     8  53 190  28
D69V4, multiclass
       clus
vv      DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  T0+T1                             3                               8
  T2                               23                              53
  T3                              104                             190
  T4                               20                              28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 46(22Q13.32) MUTATED    70  43  37
  DEL PEAK 46(22Q13.32) WILD-TYPE 182  58  39
D69V5, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  N0                            70                             182
  N1                            43                              58
  N2                            37                              39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 46(22Q13.32) MUTATED   101  28   3   0  15
  DEL PEAK 46(22Q13.32) WILD-TYPE 219  22   4   1  30
D69V6, multiclass
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  M0                            101                             219
  M1                             28                              22
  M1A                             3                               4
  M1B                             0                               1
  MX                             15                              30
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED    69  81
  DEL PEAK 46(22Q13.32) WILD-TYPE 134 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED     69   81
  DEL PEAK 46(22Q13.32) WILD-TYPE  134  146
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  FEMALE                            69                             134
  MALE                              81                             146
[1] 2 2
[1] FALSE
D69V8, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   141   9
  DEL PEAK 46(22Q13.32) WILD-TYPE 232  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    141    9
  DEL PEAK 46(22Q13.32) WILD-TYPE  232   46
                               clus
vv                              DEL PEAK 46(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                    141
  COLON MUCINOUS ADENOCARCINOMA                             9
                               clus
vv                              DEL PEAK 46(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                      232
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
D69V9, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED     1 149
  DEL PEAK 46(22Q13.32) WILD-TYPE   2 278
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED      1  149
  DEL PEAK 46(22Q13.32) WILD-TYPE    2  278
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  NO                              1                               2
  YES                           149                             278
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(22Q13.32) MUTATED   100   1  10  11
  DEL PEAK 46(22Q13.32) WILD-TYPE 205   2  14  13
D69V10, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  R0                           100                             205
  R1                             1                               2
  R2                            10                              14
  RX                            11                              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"
D69V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(22Q13.32) MUTATED                                  1     4
  DEL PEAK 46(22Q13.32) WILD-TYPE                                0     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(22Q13.32) MUTATED                          16    69
  DEL PEAK 46(22Q13.32) WILD-TYPE                        25   142
D69V12, multiclass
                                  clus
vv                                 DEL PEAK 46(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   16
  WHITE                                                       69
                                  clus
vv                                 DEL PEAK 46(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     25
  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"
